diff --git a/packages/frontend/core/src/blocksuite/ai/components/ai-chat-messages/ai-chat-messages.spec.ts b/packages/frontend/core/src/blocksuite/ai/components/ai-chat-messages/ai-chat-messages.spec.ts
index cbc4700776..c3f7e819cd 100644
--- a/packages/frontend/core/src/blocksuite/ai/components/ai-chat-messages/ai-chat-messages.spec.ts
+++ b/packages/frontend/core/src/blocksuite/ai/components/ai-chat-messages/ai-chat-messages.spec.ts
@@ -47,4 +47,50 @@ describe('AIChatMessages scrolling', () => {
 
     expect(scrollTo).toHaveBeenCalledWith({ top: 128 });
   });
+
+  test('pauses auto scroll when user scrolls away from the bottom', () => {
+    const element = {
+      canScrollDown: false,
+      scrollTop: 120,
+      _autoScrollEnabled: true,
+      _lastObservedScrollTop: 300,
+      _getDistanceFromBottom: vi.fn(() => 260),
+    } as unknown as AIChatMessages;
+
+    (AIChatMessages.prototype as any)._onScroll.call(element);
+
+    expect(element.canScrollDown).toBe(true);
+    expect((element as any)._autoScrollEnabled).toBe(false);
+    expect((element as any)._lastObservedScrollTop).toBe(120);
+  });
+
+  test('resumes auto scroll when user returns to the bottom', () => {
+    const element = {
+      canScrollDown: true,
+      scrollTop: 420,
+      _autoScrollEnabled: false,
+      _lastObservedScrollTop: 120,
+      _getDistanceFromBottom: vi.fn(() => 8),
+    } as unknown as AIChatMessages;
+
+    (AIChatMessages.prototype as any)._onScroll.call(element);
+
+    expect(element.canScrollDown).toBe(false);
+    expect((element as any)._autoScrollEnabled).toBe(true);
+  });
+
+  test('restores auto scroll when clicking the down indicator', () => {
+    const scrollToEnd = vi.fn();
+    const element = {
+      canScrollDown: true,
+      _autoScrollEnabled: false,
+      scrollToEnd,
+    } as unknown as AIChatMessages;
+
+    (AIChatMessages.prototype as any)._onDownIndicatorClick.call(element);
+
+    expect((element as any)._autoScrollEnabled).toBe(true);
+    expect(element.canScrollDown).toBe(false);
+    expect(scrollToEnd).toHaveBeenCalled();
+  });
 });
diff --git a/packages/frontend/core/src/blocksuite/ai/components/ai-chat-messages/ai-chat-messages.ts b/packages/frontend/core/src/blocksuite/ai/components/ai-chat-messages/ai-chat-messages.ts
index 28d09d1b1a..17cff0c3b8 100644
--- a/packages/frontend/core/src/blocksuite/ai/components/ai-chat-messages/ai-chat-messages.ts
+++ b/packages/frontend/core/src/blocksuite/ai/components/ai-chat-messages/ai-chat-messages.ts
@@ -16,7 +16,7 @@ import { css, html, nothing, type PropertyValues } from 'lit';
 import { property, state } from 'lit/decorators.js';
 import { classMap } from 'lit/directives/class-map.js';
 import { repeat } from 'lit/directives/repeat.js';
-import { debounce } from 'lodash-es';
+import { debounce, throttle } from 'lodash-es';
 
 import { AffineIcon } from '../../_common/icons';
 import { type AIError, AIProvider, UnauthorizedError } from '../../provider';
@@ -24,6 +24,11 @@ import { mergeStreamObjects } from '../../utils/stream-objects';
 import type { DocDisplayConfig } from '../ai-chat-chips';
 import { type ChatContextValue } from '../ai-chat-content/type';
 import type { AIReasoningConfig } from '../ai-chat-input';
+import {
+  AI_CHAT_AUTO_SCROLL_PAUSE_EVENT,
+  AI_CHAT_AUTO_SCROLL_RESUME_THRESHOLD,
+  AI_CHAT_SCROLL_DOWN_INDICATOR_THRESHOLD,
+} from './auto-scroll';
 import { AIPreloadConfig } from './preload-config';
 import {
   type HistoryMessage,
@@ -218,6 +223,10 @@ export class AIChatMessages extends WithDisposable(ShadowlessElement) {
   })
   accessor testId = 'chat-panel-messages';
 
+  private _autoScrollEnabled = true;
+
+  private _lastObservedScrollTop = 0;
+
   private get _isReasoningActive() {
     return !!this.reasoningConfig.enabled.value;
   }
@@ -243,20 +252,49 @@ export class AIChatMessages extends WithDisposable(ShadowlessElement) {
         </div>`;
   }
 
-  private readonly _onScroll = () => {
-    const { clientHeight, scrollTop, scrollHeight } = this;
-    this.canScrollDown = scrollHeight - scrollTop - clientHeight > 200;
-  };
+  private _onScroll() {
+    const { scrollTop } = this;
+    const distanceFromBottom = this._getDistanceFromBottom();
+
+    this.canScrollDown =
+      distanceFromBottom > AI_CHAT_SCROLL_DOWN_INDICATOR_THRESHOLD;
+
+    if (distanceFromBottom <= AI_CHAT_AUTO_SCROLL_RESUME_THRESHOLD) {
+      this._autoScrollEnabled = true;
+    } else if (scrollTop < this._lastObservedScrollTop) {
+      this._autoScrollEnabled = false;
+    }
+
+    this._lastObservedScrollTop = scrollTop;
+  }
 
   private readonly _debouncedOnScroll = debounce(
     this._onScroll.bind(this),
     100
   );
 
-  private readonly _onDownIndicatorClick = () => {
+  private readonly _throttledScrollToEnd = throttle(() => {
+    if (!this._autoScrollEnabled) {
+      return;
+    }
+    this.scrollToEnd();
+  }, 200);
+
+  private _onDownIndicatorClick() {
+    this._autoScrollEnabled = true;
     this.canScrollDown = false;
     this.scrollToEnd();
-  };
+  }
+
+  private _pauseAutoScroll() {
+    this._autoScrollEnabled = false;
+    requestAnimationFrame(() => this._onScroll());
+  }
+
+  private _getDistanceFromBottom() {
+    const { clientHeight, scrollTop, scrollHeight } = this;
+    return scrollHeight - scrollTop - clientHeight;
+  }
 
   protected override render() {
     const { status, error } = this.chatContextValue;
@@ -392,19 +430,39 @@ export class AIChatMessages extends WithDisposable(ShadowlessElement) {
 
     // Add scroll event listener to the host element
     this.addEventListener('scroll', this._debouncedOnScroll);
+    this.addEventListener(
+      AI_CHAT_AUTO_SCROLL_PAUSE_EVENT,
+      this._pauseAutoScroll as EventListener
+    );
     disposables.add(() => {
       this.removeEventListener('scroll', this._debouncedOnScroll);
+      this.removeEventListener(
+        AI_CHAT_AUTO_SCROLL_PAUSE_EVENT,
+        this._pauseAutoScroll as EventListener
+      );
     });
   }
 
-  protected override updated(_changedProperties: PropertyValues) {
-    if (_changedProperties.has('isHistoryLoading')) {
+  protected override updated(changedProperties: PropertyValues) {
+    if (changedProperties.has('isHistoryLoading')) {
       this.canScrollDown = false;
+      this._autoScrollEnabled = true;
+    }
+
+    if (changedProperties.has('messages')) {
+      this._onScroll();
+
+      if (this.chatContextValue.status === 'transmitting') {
+        this._throttledScrollToEnd();
+      } else if (this._autoScrollEnabled) {
+        this.scrollToEnd();
+      }
     }
 
     if (
-      _changedProperties.has('chatContextValue') &&
-      this.chatContextValue.status === 'transmitting'
+      changedProperties.has('chatContextValue') &&
+      (this.chatContextValue.status === 'success' ||
+        this.chatContextValue.status === 'error')
     ) {
       this._onScroll();
     }
diff --git a/packages/frontend/core/src/blocksuite/ai/components/ai-chat-messages/auto-scroll.ts b/packages/frontend/core/src/blocksuite/ai/components/ai-chat-messages/auto-scroll.ts
new file mode 100644
index 0000000000..ed8f1e9cd2
--- /dev/null
+++ b/packages/frontend/core/src/blocksuite/ai/components/ai-chat-messages/auto-scroll.ts
@@ -0,0 +1,6 @@
+export const AI_CHAT_AUTO_SCROLL_PAUSE_EVENT =
+  'affine-ai-chat-auto-scroll-pause';
+
+export const AI_CHAT_AUTO_SCROLL_RESUME_THRESHOLD = 32;
+
+export const AI_CHAT_SCROLL_DOWN_INDICATOR_THRESHOLD = 200;
diff --git a/packages/frontend/core/src/blocksuite/ai/components/ai-tools/doc-edit.ts b/packages/frontend/core/src/blocksuite/ai/components/ai-tools/doc-edit.ts
index d222a0095d..f66a96344a 100644
--- a/packages/frontend/core/src/blocksuite/ai/components/ai-tools/doc-edit.ts
+++ b/packages/frontend/core/src/blocksuite/ai/components/ai-tools/doc-edit.ts
@@ -21,6 +21,7 @@ import { AIProvider } from '../../provider';
 import { BlockDiffProvider } from '../../services/block-diff';
 import { diffMarkdown } from '../../utils/apply-model/markdown-diff';
 import { copyText } from '../../utils/editor-actions';
+import { AI_CHAT_AUTO_SCROLL_PAUSE_EVENT } from '../ai-chat-messages/auto-scroll';
 import type { ToolError } from './type';
 
 interface DocEditToolCall {
@@ -322,6 +323,12 @@ export class DocEditTool extends WithDisposable(ShadowlessElement) {
   }
 
   private async _toggleCollapse() {
+    this.dispatchEvent(
+      new CustomEvent(AI_CHAT_AUTO_SCROLL_PAUSE_EVENT, {
+        bubbles: true,
+        composed: true,
+      })
+    );
     this.isCollapsed = !this.isCollapsed;
   }
 
diff --git a/packages/frontend/core/src/blocksuite/ai/components/ai-tools/tool-result-card.ts b/packages/frontend/core/src/blocksuite/ai/components/ai-tools/tool-result-card.ts
index dd35489f06..e8f820ccd2 100644
--- a/packages/frontend/core/src/blocksuite/ai/components/ai-tools/tool-result-card.ts
+++ b/packages/frontend/core/src/blocksuite/ai/components/ai-tools/tool-result-card.ts
@@ -8,6 +8,8 @@ import { css, html, nothing, type TemplateResult } from 'lit';
 import { property, state } from 'lit/decorators.js';
 import { ifDefined } from 'lit/directives/if-defined.js';
 
+import { AI_CHAT_AUTO_SCROLL_PAUSE_EVENT } from '../ai-chat-messages/auto-scroll';
+
 export interface ToolResult {
   title: string | TemplateResult<1>;
   icon?: string | TemplateResult<1>;
@@ -352,6 +354,12 @@ export class ToolResultCard extends SignalWatcher(
   }
 
   private toggleCard() {
+    this.dispatchEvent(
+      new CustomEvent(AI_CHAT_AUTO_SCROLL_PAUSE_EVENT, {
+        bubbles: true,
+        composed: true,
+      })
+    );
     this.isCollapsed = !this.isCollapsed;
   }
 }