diff --git a/kernel/model/box.go b/kernel/model/box.go
index b6824168f..1a069cb00 100644
--- a/kernel/model/box.go
+++ b/kernel/model/box.go
@@ -480,6 +480,7 @@ func RefreshFileTree() {
 		util.PushErrMsg(fmt.Sprintf(Conf.Language(85), err), 5000)
 		return
 	}
+	treenode.InitBlockTree(true)
 
 	util.PushEndlessProgress(Conf.Language(35))
 	openedBoxes := Conf.GetOpenedBoxes()
diff --git a/kernel/model/conf.go b/kernel/model/conf.go
index 809eee939..31e15186e 100644
--- a/kernel/model/conf.go
+++ b/kernel/model/conf.go
@@ -502,7 +502,7 @@ func InitBoxes() {
 				}
 			}()
 
-			treenode.InitBlockTree()
+			treenode.InitBlockTree(false)
 			initialized = true
 		}
 	} else { // 大于 1 的话说明在同步阶段已经加载过了
diff --git a/kernel/model/repository.go b/kernel/model/repository.go
index eed53fea9..c1227210b 100644
--- a/kernel/model/repository.go
+++ b/kernel/model/repository.go
@@ -497,7 +497,7 @@ func syncRepo(boot, exit, byHand bool) (err error) {
 	}
 
 	start := time.Now()
-	indexBeforeSync, err := indexRepoBeforeCloudSync(repo)
+	err = indexRepoBeforeCloudSync(repo)
 	if nil != err {
 		syncDownloadErrCount++
 		planSyncAfter(fixSyncInterval)
@@ -592,21 +592,24 @@ func syncRepo(boot, exit, byHand bool) (err error) {
 
 	// 有数据变更，需要重建索引
 	var upserts, removes []string
+	var upsertTrees int
 	for _, file := range mergeResult.Upserts {
 		upserts = append(upserts, file.Path)
+		if strings.HasSuffix(file.Path, ".sy") {
+			upsertTrees++
+		}
 	}
 	for _, file := range mergeResult.Removes {
 		removes = append(removes, file.Path)
 	}
 
 	if boot && gulu.File.IsExist(util.BlockTreePath) {
-		treenode.InitBlockTree()
+		treenode.InitBlockTree(false)
 	}
 
 	cache.ClearDocsIAL() // 同步后文档树文档图标没有更新 https://github.com/siyuan-note/siyuan/issues/4939
 
-	fullReindex := 0.2 < float64(len(upserts))/float64(len(indexBeforeSync.Files))
-	if fullReindex { // 如果更新的文件比较多则全量重建索引
+	if needFullReindex(upsertTrees) { // 改进同步后全量重建索引判断 https://github.com/siyuan-note/siyuan/issues/5764
 		RefreshFileTree()
 		return
 	}
@@ -626,10 +629,14 @@ func syncRepo(boot, exit, byHand bool) (err error) {
 	return
 }
 
-func indexRepoBeforeCloudSync(repo *dejavu.Repo) (index *entity.Index, err error) {
+func needFullReindex(upsertTrees int) bool {
+	return 0.2 < float64(upsertTrees)/float64(treenode.CountTrees())
+}
+
+func indexRepoBeforeCloudSync(repo *dejavu.Repo) (err error) {
 	start := time.Now()
 	latest, _ := repo.Latest()
-	index, err = repo.Index("[Sync] Cloud sync", map[string]interface{}{
+	index, err := repo.Index("[Sync] Cloud sync", map[string]interface{}{
 		dejavu.CtxPushMsg: dejavu.CtxPushMsgToStatusBar,
 	})
 	if nil != err {
diff --git a/kernel/treenode/blocktree.go b/kernel/treenode/blocktree.go
index 3cf551a40..455484c6f 100644
--- a/kernel/treenode/blocktree.go
+++ b/kernel/treenode/blocktree.go
@@ -47,6 +47,15 @@ type BlockTree struct {
 	HPath    string // 文档逻辑路径
 }
 
+func CountTrees() (ret int) {
+	roots := map[string]bool{}
+	for _, b := range blockTrees {
+		roots[b.RootID] = true
+	}
+	ret = len(roots)
+	return
+}
+
 func GetBlockTrees() map[string]*BlockTree {
 	return blockTrees
 }
@@ -218,11 +227,24 @@ func AutoFlushBlockTree() {
 	}
 }
 
-func InitBlockTree() {
+func InitBlockTree(force bool) {
 	start := time.Now()
 
 	if nil == blocktreeFileLock {
 		blocktreeFileLock = flock.New(util.BlockTreePath)
+	} else {
+		if force {
+			err := blocktreeFileLock.Unlock()
+			if nil != err {
+				logging.LogErrorf("unlock blocktree file failed: %s", err)
+			}
+			err = os.RemoveAll(util.BlockTreePath)
+			if nil != err {
+				logging.LogErrorf("remove blocktree file failed: %s", err)
+			}
+			blocktreeFileLock = flock.New(util.BlockTreePath)
+			return
+		}
 	}
 
 	var err error
@@ -247,6 +269,7 @@ func InitBlockTree() {
 	blockTreesLock.Lock()
 	if err = msgpack.Unmarshal(data, &blockTrees); nil != err {
 		logging.LogErrorf("unmarshal block tree failed: %s", err)
+		blocktreeFileLock.Unlock()
 		if err = os.RemoveAll(util.BlockTreePath); nil != err {
 			logging.LogErrorf("removed corrupted block tree failed: %s", err)
 		}