diff --git a/frontend-web/src/components/workspace/messages/message-group.tsx b/frontend-web/src/components/workspace/messages/message-group.tsx
index f4909372..013639fe 100644
--- a/frontend-web/src/components/workspace/messages/message-group.tsx
+++ b/frontend-web/src/components/workspace/messages/message-group.tsx
@@ -15,7 +15,7 @@ import {
   SquareTerminalIcon,
   WrenchIcon,
 } from "lucide-react";
-import { useEffect, useMemo, useState } from "react";
+import { useCallback, useEffect, useMemo, useState, type AnchorHTMLAttributes } from "react";
 
 import {
   ChainOfThought,
@@ -58,6 +58,7 @@ import { useRehypeSplitWordsIntoSpans } from "@/core/rehype";
 import { useLocalSettings } from "@/core/settings";
 import { useSkills } from "@/core/skills/hooks";
 import {
+  applyInlineCitations,
   buildSkillDisplayMap,
   findDisplayConfigForTool,
   isDisplaySamplePayload,
@@ -71,6 +72,7 @@ import { env } from "@/env";
 import { cn } from "@/lib/utils";
 
 import { useArtifactsOptional } from "../artifacts";
+import { CitationLink } from "../citations/citation-link";
 import { FlipDisplay } from "../flip-display";
 import { Tooltip } from "../tooltip";
 import {
@@ -79,15 +81,18 @@ import {
 } from "../skill-display-sources";
 
 import { MarkdownContent } from "./markdown-content";
+import { SingleRoundRagCitationDialog } from "./message-list-item";
 
 export function MessageGroup({
   className,
   messages,
   isLoading = false,
+  displaySources = [],
 }: {
   className?: string;
   messages: Message[];
   isLoading?: boolean;
+  displaySources?: RuntimeDisplaySource[];
 }) {
   const { t } = useI18n();
   const [showAbove, setShowAbove] = useState(
@@ -124,11 +129,29 @@ export function MessageGroup({
     }
   }, [lastToolCallStep, steps]);
   const rehypePlugins = useRehypeSplitWordsIntoSpans(isLoading);
+  const [selectedCitation, setSelectedCitation] =
+    useState<RuntimeDisplaySource | null>(null);
+  const handleCitationClick = useCallback(
+    (referenceId: string) => {
+      const referenceIndex = Number(referenceId);
+      if (!Number.isInteger(referenceIndex) || referenceIndex < 1) return;
+      const source =
+        displaySources.find((item) => item.index === referenceIndex) ??
+        displaySources[referenceIndex - 1];
+      if (source) setSelectedCitation(source);
+    },
+    [displaySources],
+  );
+  const reasoningId =
+    lastReasoningStep?.id ??
+    messages.find((message) => message.type === "ai")?.id;
   return (
-    <ChainOfThought
-      className={cn("w-full gap-2 rounded-lg border p-0.5", className)}
-      open={true}
-    >
+    <>
+      <ChainOfThought
+        className={cn("w-full gap-2 rounded-lg border p-0.5", className)}
+        data-reference-batch-id={reasoningId}
+        open={true}
+      >
       {aboveLastToolCallSteps.length > 0 && (
         <Button
           key="above"
@@ -163,10 +186,12 @@ export function MessageGroup({
                 <ChainOfThoughtStep
                   key={step.id}
                   label={
-                    <MarkdownContent
+                    <StepReasoningMarkdown
                       content={step.reasoning ?? ""}
+                      displaySources={displaySources}
                       isLoading={isLoading}
                       rehypePlugins={rehypePlugins}
+                      onCitationClick={handleCitationClick}
                     />
                   }
                 ></ChainOfThoughtStep>
@@ -223,10 +248,12 @@ export function MessageGroup({
               <ChainOfThoughtStep
                 key={lastReasoningStep.id}
                 label={
-                  <MarkdownContent
+                  <StepReasoningMarkdown
                     content={lastReasoningStep.reasoning ?? ""}
+                    displaySources={displaySources}
                     isLoading={isLoading}
                     rehypePlugins={rehypePlugins}
+                    onCitationClick={handleCitationClick}
                   />
                 }
               ></ChainOfThoughtStep>
@@ -234,7 +261,60 @@ export function MessageGroup({
           )}
         </>
       )}
-    </ChainOfThought>
+      </ChainOfThought>
+      <SingleRoundRagCitationDialog
+        source={selectedCitation}
+        onOpenChange={(open) => {
+          if (!open) setSelectedCitation(null);
+        }}
+      />
+    </>
+  );
+}
+
+function StepReasoningMarkdown({
+  content,
+  displaySources,
+  isLoading,
+  rehypePlugins,
+  onCitationClick,
+}: {
+  content: string;
+  displaySources: RuntimeDisplaySource[];
+  isLoading: boolean;
+  rehypePlugins: ReturnType<typeof useRehypeSplitWordsIntoSpans>;
+  onCitationClick: (referenceId: string) => void;
+}) {
+  const markdown = useMemo(
+    () =>
+      applyInlineCitations(content, displaySources, { appendSummary: false }),
+    [content, displaySources],
+  );
+  const components = useMemo(() => {
+    if (displaySources.length === 0) return undefined;
+    return {
+      a: ({ href, ...props }: AnchorHTMLAttributes<HTMLAnchorElement>) => {
+        if (href?.startsWith("#reference-")) {
+          return (
+            <CitationLink
+              href={href}
+              {...props}
+              onReferenceClick={onCitationClick}
+            />
+          );
+        }
+        return <a href={href} {...props} />;
+      },
+    };
+  }, [displaySources.length, onCitationClick]);
+
+  return (
+    <MarkdownContent
+      content={markdown}
+      isLoading={isLoading}
+      rehypePlugins={rehypePlugins}
+      components={components}
+    />
   );
 }
 
diff --git a/frontend-web/src/components/workspace/messages/message-list-item.tsx b/frontend-web/src/components/workspace/messages/message-list-item.tsx
index 87d33005..3e138bbd 100644
--- a/frontend-web/src/components/workspace/messages/message-list-item.tsx
+++ b/frontend-web/src/components/workspace/messages/message-list-item.tsx
@@ -695,13 +695,6 @@ function MessageContent_({
     const withCitations = applyInlineCitations(rawContent ?? '', displaySources);
     return stripIncompleteCitationMarker(withCitations);
   }, [rawContent, isHuman, displaySources]);
-  const reasoningToDisplay = useMemo(() => {
-    if (!reasoningContent) return '';
-    const withCitations = applyInlineCitations(reasoningContent, displaySources, {
-      appendSummary: false,
-    });
-    return stripIncompleteCitationMarker(withCitations);
-  }, [reasoningContent, displaySources]);
   const markdownRehypePlugins = useMemo(
     () => [...rehypePlugins, [rehypeKatex, { output: 'html' as const }]],
     [rehypePlugins],
@@ -735,6 +728,23 @@ function MessageContent_({
     );
   }
 
+  // Reasoning-only AI message (no main response content yet)
+  if (!isHuman && reasoningContent && !rawContent && !multiRoundTrace) {
+    return (
+      <AIElementMessageContent className={className}>
+        <Reasoning isStreaming={isLoading}>
+          <ReasoningTrigger />
+          <ReasoningContent>{reasoningContent}</ReasoningContent>
+        </Reasoning>
+        <MessageTokenUsage
+          enabled={tokenUsageEnabled}
+          isLoading={isLoading}
+          message={message}
+        />
+      </AIElementMessageContent>
+    );
+  }
+
   if (isHuman) {
     // Only the user's own question carries a delete affordance, and only once
     // it exists server-side (real, non-optimistic id). Deleting it cascades to
@@ -770,24 +780,6 @@ function MessageContent_({
       <AIElementMessageContent className={className}>
         {filesList}
         <div data-reference-batch-id={message.id} className="contents">
-          {reasoningToDisplay && !multiRoundTrace && (
-            <Reasoning isStreaming={isLoading && !contentToDisplay}>
-              <ReasoningTrigger />
-              <ReasoningContent>
-                {isSingleRoundRag || displaySources.length > 0 ? (
-                  <MarkdownContent
-                    content={reasoningToDisplay}
-                    isLoading={isLoading}
-                    rehypePlugins={markdownRehypePlugins}
-                    components={components}
-                    className="text-muted-foreground text-sm"
-                  />
-                ) : (
-                  reasoningToDisplay
-                )}
-              </ReasoningContent>
-            </Reasoning>
-          )}
           {multiRoundTrace ? (
             <MultiRoundRagContent
               trace={multiRoundTrace}
@@ -797,7 +789,7 @@ function MessageContent_({
               rehypePlugins={markdownRehypePlugins}
               components={components}
             />
-          ) : contentToDisplay ? (
+          ) : (
             <AssistantDisplayContent
               content={contentToDisplay}
               displaySources={displaySources}
@@ -806,7 +798,7 @@ function MessageContent_({
               rehypePlugins={markdownRehypePlugins}
               components={components}
             />
-          ) : null}
+          )}
         </div>
         {(isSingleRoundRag || isMultiRoundRag) && displaySources.length > 0 && (
           <FrontendRagSourcesPanel
@@ -905,7 +897,7 @@ function FrontendRagSourcesPanel({
   );
 }
 
-function SingleRoundRagCitationDialog({
+export function SingleRoundRagCitationDialog({
   source,
   onOpenChange,
 }: {
diff --git a/frontend-web/src/components/workspace/messages/message-list.tsx b/frontend-web/src/components/workspace/messages/message-list.tsx
index 016168d8..678a83a3 100644
--- a/frontend-web/src/components/workspace/messages/message-list.tsx
+++ b/frontend-web/src/components/workspace/messages/message-list.tsx
@@ -11,8 +11,8 @@ import {
 } from "@/components/ai-elements/conversation";
 import { Button } from "@/components/ui/button";
 import { Textarea } from "@/components/ui/textarea";
-import { rememberAskTimes, useChatAskTimes } from "@/core/chat-timestamps";
-import { useDocumentRewritePresentation } from "@/core/document-rewrite/context";
+import { rememberAskTimes, useChatAskTimes } from "@/core/chat-timestamps";
+import { useDocumentRewritePresentation } from "@/core/document-rewrite/context";
 import { useI18n } from "@/core/i18n/hooks";
 import {
   extractContentFromMessage,
@@ -46,8 +46,8 @@ import { getQuestionAnchorId } from "../question-navigator";
 import { StreamingIndicator } from "../streaming-indicator";
 
 import { ReferenceBatchesContext, ThreadContext } from "./context";
-import { MarkdownContent } from "./markdown-content";
-import { DocumentRewriteTimeline } from "./document-rewrite-timeline";
+import { MarkdownContent } from "./markdown-content";
+import { DocumentRewriteTimeline } from "./document-rewrite-timeline";
 import { MessageGroup } from "./message-group";
 import { MessageListItem } from "./message-list-item";
 import {
@@ -112,10 +112,10 @@ export function MessageList({
   onSetupWritingApprove,
   onSetupWritingReject,
   onSetupWritingStart,
-  researchApprovalSlot,
-  onOpenArtifact,
-  onDownloadArtifact,
-}: {
+  researchApprovalSlot,
+  onOpenArtifact,
+  onDownloadArtifact,
+}: {
   className?: string;
   contentClassName?: string;
   fitMessageRowsToContent?: boolean;
@@ -138,23 +138,23 @@ export function MessageList({
   /** 审批卡「直接开始写作」回调：应用配置（含已确认大纲）并立即启动写作流程（仅写作页提供，模板编辑等场景缺省隐藏该按钮）。 */
   onSetupWritingStart?: (payload: SetupWritingApprovalPayload) => void | Promise<void>;
   /**
-   * 深度研究的交互卡插槽（报告配置、计划确认、失败重试）：workbench 向
-   * displayThread 注入带 `additional_kwargs.setup_research_approval` 的虚拟 ai
-   * 消息。撰写步骤和完成摘要不走此插槽，而是分别复用原生 tool-call 步骤条和
-   * assistant 消息行；不传该 slot 时普通对话/AI 写作零行为变化。
+   * 深度研究的交互卡插槽（报告配置、计划确认、失败重试）：workbench 向
+   * displayThread 注入带 `additional_kwargs.setup_research_approval` 的虚拟 ai
+   * 消息。撰写步骤和完成摘要不走此插槽，而是分别复用原生 tool-call 步骤条和
+   * assistant 消息行；不传该 slot 时普通对话/AI 写作零行为变化。
    */
-  researchApprovalSlot?: (message: Message) => React.ReactNode;
-  onOpenArtifact?: (filepath: string) => void;
-  /** Host override for downloading virtual/session-owned files in a present-files card. */
-  onDownloadArtifact?: (filepath: string) => void | Promise<void>;
+  researchApprovalSlot?: (message: Message) => React.ReactNode;
+  onOpenArtifact?: (filepath: string) => void;
+  /** Host override for downloading virtual/session-owned files in a present-files card. */
+  onDownloadArtifact?: (filepath: string) => void | Promise<void>;
 }) {
   const baseRehypePlugins = useRehypeSplitWordsIntoSpans(thread.isLoading);
   const rehypePlugins = useMemo(
     () => (extraRehypePlugins?.length ? [...baseRehypePlugins, ...extraRehypePlugins] : baseRehypePlugins),
     [baseRehypePlugins, extraRehypePlugins],
   );
-  const updateSubtask = useUpdateSubtask();
-  const documentRewritePresentation = useDocumentRewritePresentation();
+  const updateSubtask = useUpdateSubtask();
+  const documentRewritePresentation = useDocumentRewritePresentation();
   const { t } = useI18n();
   const threadContext = useContext(ThreadContext);
   // Read-only contexts (public share, mock previews) must not offer deletion.
@@ -194,7 +194,7 @@ export function MessageList({
           : ({ ...message, content: override } as Message);
       });
   }, [messageContentOverrides, thread.messages]);
-  const messages = useMemo(
+  const messages = useMemo(
     () => {
       const externalHidden = externallyHiddenMessageIds ?? new Set<string>();
       return hiddenMessageIds.size === 0 && externalHidden.size === 0
@@ -205,9 +205,9 @@ export function MessageList({
               (!hiddenMessageIds.has(m.id) && !externalHidden.has(m.id)),
           );
     },
-    [allMessages, externallyHiddenMessageIds, hiddenMessageIds],
-  );
-  const documentRewriteItems = documentRewritePresentation?.forThread(threadId) ?? [];
+    [allMessages, externallyHiddenMessageIds, hiddenMessageIds],
+  );
+  const documentRewriteItems = documentRewritePresentation?.forThread(threadId) ?? [];
 
   const askTimes = useChatAskTimes();
 
@@ -255,15 +255,15 @@ export function MessageList({
   const [settings] = useLocalSettings();
   const ragModeEnabled =
     settings.display.ragModeEnabled || isThreadRagModeLocked(threadId);
-  const hasSingleRoundRag = useMemo(
+  const hasSingleRoundRag = useMemo(
     () =>
       messages.some(
         (message) =>
           isSingleRoundRagMessage(message) || isMultiRoundRagMessage(message),
       ),
-    [messages],
-  );
-  const referencesEnabled = ragModeEnabled || hasSingleRoundRag;
+    [messages],
+  );
+  const referencesEnabled = ragModeEnabled || hasSingleRoundRag;
   const { skills } = useSkills();
   const skillDisplayMap = useMemo(
     () => (referencesEnabled ? buildSkillDisplayMap(skills) : new Map()),
@@ -322,6 +322,32 @@ export function MessageList({
     return map;
   }, [thread.messages]);
 
+  const resolveDisplaySources = useCallback(
+    (msg: Message | undefined): RuntimeDisplaySource[] => {
+      if (!referencesEnabled || !msg || msg.type !== "ai") return [];
+      const batchSources =
+        referenceBatches.find((batch) => batch.assistant_message_id === msg.id)
+          ?.sources ?? [];
+      const frontendRagSources = msg.id
+        ? frontendRagSourcesByAiId.get(msg.id) ?? []
+        : [];
+      if (batchSources.length > 0) return batchSources;
+      if (frontendRagSources.length > 0) return frontendRagSources;
+      return collectRuntimeDisplaySources(messages, skillDisplayMap, {
+        afterMessageId: findPreviousHumanMessageId(messages, msg.id),
+        beforeMessageId: msg.id,
+        includeBeforeMessage: true,
+      });
+    },
+    [
+      frontendRagSourcesByAiId,
+      messages,
+      referenceBatches,
+      referencesEnabled,
+      skillDisplayMap,
+    ],
+  );
+
   // Track which clarification messages are still awaiting an answer.
   // Pending = clarification tool messages that appear after the last human message
   // (no user reply has been sent for them yet).
@@ -436,47 +462,29 @@ export function MessageList({
       className={cn("flex size-full flex-col justify-center", className)}
     >
       <ScrollToBottomOnUserMessage threadId={threadId} messages={messages} />
-      <ConversationContent
-        className={cn(
-          "mx-auto w-full max-w-(--container-width-lg)",
-          hasSingleRoundRag ? "gap-4 pt-4" : "gap-8 pt-12",
-          contentClassName,
-        )}
+      <ConversationContent
+        className={cn(
+          "mx-auto w-full max-w-(--container-width-lg)",
+          hasSingleRoundRag ? "gap-4 pt-4" : "gap-8 pt-12",
+          contentClassName,
+        )}
       >
         <MessageMetricsProvider messages={messages} isLoading={thread.isLoading}>
-        {groupMessages(messages, (group) => {
+        {groupMessages(messages, (group) => {
           if (group.type === "human" || group.type === "assistant") {
-            return group.messages.map((msg) => {
-              // 深度研究的报告摘要由独立 SSE 作业驱动；把它接入既有 assistant 流式状态，
-              // 便于 Streamdown 在每次 summary_delta 到达时立即更新该普通消息行。
-              const messageIsLoading =
-                thread.isLoading ||
-                msg.additional_kwargs?.deep_research_summary_streaming === true ||
-                msg.additional_kwargs?.deep_research_follow_up_streaming === true;
-              const isAssistantMessage =
+            return group.messages.map((msg) => {
+              // 深度研究的报告摘要由独立 SSE 作业驱动；把它接入既有 assistant 流式状态，
+              // 便于 Streamdown 在每次 summary_delta 到达时立即更新该普通消息行。
+              const messageIsLoading =
+                thread.isLoading ||
+                msg.additional_kwargs?.deep_research_summary_streaming === true ||
+                msg.additional_kwargs?.deep_research_follow_up_streaming === true;
+              const isAssistantMessage =
                 referencesEnabled &&
                 group.type === "assistant" &&
                 msg.type === "ai";
-              const batchSources = isAssistantMessage
-                ? referenceBatches.find(
-                    (batch) => batch.assistant_message_id === msg.id,
-                  )?.sources ?? []
-                : [];
-              // 单轮/多轮 RAG 的参考资料来自隐藏的 tool 消息，优先于通用扫描。
-              const frontendRagSources =
-                isAssistantMessage && msg.id
-                  ? frontendRagSourcesByAiId.get(msg.id) ?? []
-                  : [];
               const displaySources = isAssistantMessage
-                ? batchSources.length > 0
-                  ? batchSources
-                  : frontendRagSources.length > 0
-                    ? frontendRagSources
-                    : collectRuntimeDisplaySources(messages, skillDisplayMap, {
-                        afterMessageId: findPreviousHumanMessageId(messages, msg.id),
-                        beforeMessageId: msg.id,
-                        includeBeforeMessage: true,
-                      })
+                ? resolveDisplaySources(msg)
                 : [];
               return (
                 <MessageListItem
@@ -486,9 +494,9 @@ export function MessageList({
                     msg.type === "human"
                       ? getQuestionAnchorId(msg, messages.indexOf(msg))
                       : undefined
-                  }
-                  message={msg}
-                  isLoading={messageIsLoading}
+                  }
+                  message={msg}
+                  isLoading={messageIsLoading}
                   threadId={threadId}
                   tokenUsageEnabled={tokenUsageEnabled}
                   displaySources={displaySources}
@@ -584,8 +592,8 @@ export function MessageList({
               </div>
             ) : null;
           } else if (group.type === "assistant:research-approval") {
-            // 深度研究交互卡（配置/计划确认/失败重试）：宿主不传渲染函数时该
-            // 分组不渲染。撰写步骤和完成摘要会经过普通的 processing/assistant 分组。
+            // 深度研究交互卡（配置/计划确认/失败重试）：宿主不传渲染函数时该
+            // 分组不渲染。撰写步骤和完成摘要会经过普通的 processing/assistant 分组。
             const message = group.messages[0];
             return researchApprovalSlot && message ? (
               <div key={group.id} className="w-full pb-2">
@@ -611,11 +619,11 @@ export function MessageList({
                   />
                 )}
                 <ArtifactFileList
-                  files={files}
-                  threadId={threadId}
-                  onOpenArtifact={onOpenArtifact}
-                  onDownloadArtifact={onDownloadArtifact}
-                />
+                  files={files}
+                  threadId={threadId}
+                  onOpenArtifact={onOpenArtifact}
+                  onDownloadArtifact={onDownloadArtifact}
+                />
                 <MessageTokenUsageList
                   enabled={tokenUsageEnabled}
                   isLoading={thread.isLoading}
@@ -683,6 +691,7 @@ export function MessageList({
                     key={"thinking-group-" + message.id}
                     messages={[message]}
                     isLoading={thread.isLoading}
+                    displaySources={resolveDisplaySources(message)}
                   />,
                 );
               }
@@ -726,11 +735,15 @@ export function MessageList({
               message.type === "ai" &&
               (hasToolCalls(message) ? true : !hasContent(message)),
           );
+          const processingAi = [...group.messages]
+            .reverse()
+            .find((message) => message.type === "ai");
           return (
             <div key={"group-" + group.id} className="w-full">
               <MessageGroup
                 messages={group.messages}
                 isLoading={thread.isLoading}
+                displaySources={resolveDisplaySources(processingAi)}
               />
               <MessageTokenUsageList
                 enabled={tokenUsageEnabled}
@@ -739,11 +752,11 @@ export function MessageList({
               />
             </div>
           );
-        })}
-        {documentRewriteItems.map((item) => (
-          <DocumentRewriteTimeline key={item.id} item={item} />
-        ))}
-        {thread.isLoading && <StreamingIndicator className="my-4" />}
+        })}
+        {documentRewriteItems.map((item) => (
+          <DocumentRewriteTimeline key={item.id} item={item} />
+        ))}
+        {thread.isLoading && <StreamingIndicator className="my-4" />}
         <div style={{ height: `${paddingBottom}px` }} />
         </MessageMetricsProvider>
       </ConversationContent>