diff --git a/web/app/components/workflow/skill/editor/skill-editor/plugins/file-reference-block/component.tsx b/web/app/components/workflow/skill/editor/skill-editor/plugins/file-reference-block/component.tsx
index 048a7d4027..2240c70169 100644
--- a/web/app/components/workflow/skill/editor/skill-editor/plugins/file-reference-block/component.tsx
+++ b/web/app/components/workflow/skill/editor/skill-editor/plugins/file-reference-block/component.tsx
@@ -1,6 +1,7 @@
 import type { LexicalNode } from 'lexical'
 import type { FileAppearanceType } from '@/app/components/base/file-uploader/types'
 import type { TreeNodeData } from '@/app/components/workflow/skill/type'
+import type { AppAssetTreeView } from '@/types/app-asset'
 import { useLexicalComposerContext } from '@lexical/react/LexicalComposerContext'
 import { RiAlertFill, RiFolderLine } from '@remixicon/react'
 import { $getNodeByKey } from 'lexical'
@@ -16,8 +17,10 @@ import {
 } from '@/app/components/base/portal-to-follow-elem'
 import { useSelectOrDelete } from '@/app/components/base/prompt-editor/hooks'
 import Tooltip from '@/app/components/base/tooltip'
+import { START_TAB_ID } from '@/app/components/workflow/skill/constants'
 import { useSkillAssetNodeMap } from '@/app/components/workflow/skill/hooks/use-skill-asset-tree'
 import { getFileIconType } from '@/app/components/workflow/skill/utils/file-utils'
+import { useStore } from '@/app/components/workflow/store'
 import { cn } from '@/utils/classnames'
 import { FilePickerPanel } from '../file-picker-panel'
 import FilePreviewPanel from './file-preview-panel'
@@ -28,10 +31,16 @@ type FileReferenceBlockProps = {
   resourceId: string
 }
 
+type SkillFileMetadata = {
+  files?: Record<string, AppAssetTreeView>
+}
+
 const FileReferenceBlock = ({ nodeKey, resourceId }: FileReferenceBlockProps) => {
   const [editor] = useLexicalComposerContext()
   const [ref, isSelected] = useSelectOrDelete(nodeKey)
   const { data: nodeMap, isLoading: isNodeMapLoading } = useSkillAssetNodeMap()
+  const activeTabId = useStore(s => s.activeTabId)
+  const fileMetadata = useStore(s => s.fileMetadata)
   const [open, setOpen] = useState(false)
   const [previewOpen, setPreviewOpen] = useState(false)
   const [previewStyle, setPreviewStyle] = useState<React.CSSProperties | null>(null)
@@ -40,7 +49,16 @@ const FileReferenceBlock = ({ nodeKey, resourceId }: FileReferenceBlockProps) =>
   const { t } = useTranslation()
   const isInteractive = editor.isEditable()
 
-  const currentNode = useMemo(() => nodeMap?.get(resourceId), [nodeMap, resourceId])
+  const metadataFiles = useMemo(() => {
+    if (!activeTabId || activeTabId === START_TAB_ID)
+      return undefined
+    const metadata = fileMetadata.get(activeTabId) as SkillFileMetadata | undefined
+    return metadata?.files
+  }, [activeTabId, fileMetadata])
+
+  const treeNode = useMemo(() => nodeMap?.get(resourceId), [nodeMap, resourceId])
+  const metadataNode = useMemo(() => metadataFiles?.[resourceId], [metadataFiles, resourceId])
+  const currentNode = useMemo(() => treeNode ?? metadataNode, [metadataNode, treeNode])
 
   const fallbackName = useMemo(() => {
     if (resourceId.includes('/')) {
@@ -50,7 +68,7 @@ const FileReferenceBlock = ({ nodeKey, resourceId }: FileReferenceBlockProps) =>
     return resourceId.slice(0, 8)
   }, [resourceId])
   const isFolder = currentNode?.node_type === 'folder'
-  const isMissing = !isNodeMapLoading && !currentNode
+  const isMissing = !isNodeMapLoading && !treeNode
   const shouldPreview = isPreviewEnabled && !isFolder && !isMissing
   const displayName = currentNode?.name ?? fallbackName
   const iconType = !isFolder && currentNode
diff --git a/web/app/components/workflow/skill/editor/skill-editor/plugins/tool-block/component.tsx b/web/app/components/workflow/skill/editor/skill-editor/plugins/tool-block/component.tsx
index 6e88dd633e..18b0f82e30 100644
--- a/web/app/components/workflow/skill/editor/skill-editor/plugins/tool-block/component.tsx
+++ b/web/app/components/workflow/skill/editor/skill-editor/plugins/tool-block/component.tsx
@@ -2,6 +2,7 @@ import type { PluginDetail } from '@/app/components/plugins/types'
 import type { Emoji } from '@/app/components/tools/types'
 import type { ToolValue } from '@/app/components/workflow/block-selector/types'
 import type { ToolWithProvider } from '@/app/components/workflow/types'
+import type { AppAssetTreeView } from '@/types/app-asset'
 import { useLexicalComposerContext } from '@lexical/react/LexicalComposerContext'
 import { RiAlertFill } from '@remixicon/react'
 import * as React from 'react'
@@ -73,6 +74,7 @@ type ToolConfigMetadata = {
 
 type SkillFileMetadata = {
   tools?: Record<string, ToolConfigMetadata>
+  files?: Record<string, AppAssetTreeView>
 }
 
 const getVarKindType = (type: FormTypeEnum | string) => {
diff --git a/web/app/components/workflow/skill/file-content-panel.tsx b/web/app/components/workflow/skill/file-content-panel.tsx
index c6e101ac59..ec2f0825a5 100644
--- a/web/app/components/workflow/skill/file-content-panel.tsx
+++ b/web/app/components/workflow/skill/file-content-panel.tsx
@@ -1,7 +1,9 @@
 'use client'
 
 import type { OnMount } from '@monaco-editor/react'
+import type { AppAssetTreeView } from '@/types/app-asset'
 import { loader } from '@monaco-editor/react'
+import isDeepEqual from 'fast-deep-equal'
 import dynamic from 'next/dynamic'
 import * as React from 'react'
 import { useCallback, useEffect, useRef, useState } from 'react'
@@ -26,6 +28,23 @@ import { getFileLanguage } from './utils/file-utils'
 import MediaFilePreview from './viewer/media-file-preview'
 import UnsupportedFileDownload from './viewer/unsupported-file-download'
 
+type SkillFileMetadata = {
+  files?: Record<string, AppAssetTreeView>
+}
+
+const extractFileReferenceIds = (content: string) => {
+  const ids = new Set<string>()
+  const regex = /§\[file\]\.\[app\]\.\[([a-fA-F0-9-]{36})\]§/g
+  let match: RegExpExecArray | null
+  match = regex.exec(content)
+  while (match !== null) {
+    if (match[1])
+      ids.add(match[1])
+    match = regex.exec(content)
+  }
+  return ids
+}
+
 const SQLiteFilePreview = dynamic(
   () => import('./viewer/sqlite-file-preview'),
   { ssr: false, loading: () => <Loading type="area" /> },
@@ -101,6 +120,34 @@ const FileContentPanel = () => {
     clearDraftMetadata(fileTabId)
   }, [fileTabId, isMetadataDirty, fileContent, storeApi])
 
+  const updateFileReferenceMetadata = useCallback((content: string) => {
+    if (!fileTabId)
+      return
+
+    const referenceIds = extractFileReferenceIds(content)
+    const metadata = (currentMetadata || {}) as SkillFileMetadata
+    const existingFiles = metadata.files || {}
+    const nextFiles: Record<string, AppAssetTreeView> = {}
+
+    referenceIds.forEach((id) => {
+      const node = nodeMap?.get(id)
+      if (node)
+        nextFiles[id] = node
+      else if (existingFiles[id])
+        nextFiles[id] = existingFiles[id]
+    })
+
+    const nextMetadata: SkillFileMetadata = { ...metadata }
+    if (Object.keys(nextFiles).length > 0)
+      nextMetadata.files = nextFiles
+    else if ('files' in nextMetadata)
+      delete nextMetadata.files
+
+    if (isDeepEqual(metadata, nextMetadata))
+      return
+    storeApi.getState().setDraftMetadata(fileTabId, nextMetadata)
+  }, [currentMetadata, fileTabId, nodeMap, storeApi])
+
   const handleEditorChange = useCallback((value: string | undefined) => {
     if (!fileTabId || !isEditable)
       return
@@ -110,9 +157,9 @@ const FileContentPanel = () => {
       storeApi.getState().clearDraftContent(fileTabId)
     else
       storeApi.getState().setDraftContent(fileTabId, newValue)
-
+    updateFileReferenceMetadata(newValue)
     storeApi.getState().pinTab(fileTabId)
-  }, [fileTabId, isEditable, originalContent, storeApi])
+  }, [fileTabId, isEditable, originalContent, storeApi, updateFileReferenceMetadata])
 
   const { saveFile, registerFallback, unregisterFallback } = useSkillSaveManager()
   const handleLeaderSync = useCallback(() => {