diff --git a/weed/filer/empty_folder_cleanup/empty_folder_cleaner.go b/weed/filer/empty_folder_cleanup/empty_folder_cleaner.go
index f7d7b8864..d98dd5ee6 100644
--- a/weed/filer/empty_folder_cleanup/empty_folder_cleaner.go
+++ b/weed/filer/empty_folder_cleanup/empty_folder_cleaner.go
@@ -9,6 +9,8 @@ import (
 	"github.com/seaweedfs/seaweedfs/weed/cluster/lock_manager"
 	"github.com/seaweedfs/seaweedfs/weed/glog"
 	"github.com/seaweedfs/seaweedfs/weed/pb"
+	"github.com/seaweedfs/seaweedfs/weed/pb/filer_pb"
+	"github.com/seaweedfs/seaweedfs/weed/s3api/s3_constants"
 	"github.com/seaweedfs/seaweedfs/weed/util"
 )
 
@@ -24,11 +26,13 @@ const (
 type FilerOperations interface {
 	CountDirectoryEntries(ctx context.Context, dirPath util.FullPath, limit int) (count int, err error)
 	DeleteEntryMetaAndData(ctx context.Context, p util.FullPath, isRecursive, ignoreRecursiveError, shouldDeleteChunks, isFromOtherCluster bool, signatures []int32, ifNotModifiedAfter int64) error
+	GetEntryAttributes(ctx context.Context, p util.FullPath) (attributes map[string][]byte, err error)
 }
 
 // folderState tracks the state of a folder for empty folder cleanup
 type folderState struct {
 	roughCount  int       // Cached rough count (up to maxCountCheck)
+	isImplicit  *bool     // Tri-state boolean: nil (unknown), true (implicit), false (explicit)
 	lastAddTime time.Time // Last time an item was added
 	lastDelTime time.Time // Last time an item was deleted
 	lastCheck   time.Time // Last time we checked the actual count
@@ -265,8 +269,47 @@ func (efc *EmptyFolderCleaner) executeCleanup(folder string) {
 		return
 	}
 
-	// Check if folder is actually empty (count up to maxCountCheck)
+	// Check for explicit implicit_dir attribute
+	// First check cache
 	ctx := context.Background()
+	efc.mu.RLock()
+	var cachedImplicit *bool
+	if state, exists := efc.folderCounts[folder]; exists {
+		cachedImplicit = state.isImplicit
+	}
+	efc.mu.RUnlock()
+
+	var isImplicit bool
+	if cachedImplicit != nil {
+		isImplicit = *cachedImplicit
+	} else {
+		// Not cached, check filer
+		attrs, err := efc.filer.GetEntryAttributes(ctx, util.FullPath(folder))
+		if err != nil {
+			if err == filer_pb.ErrNotFound {
+				return
+			}
+			glog.V(2).Infof("EmptyFolderCleaner: error getting attributes for %s: %v", folder, err)
+			return
+		}
+
+		isImplicit = attrs != nil && string(attrs[s3_constants.ExtS3ImplicitDir]) == "true"
+
+		// Update cache
+		efc.mu.Lock()
+		if _, exists := efc.folderCounts[folder]; !exists {
+			efc.folderCounts[folder] = &folderState{}
+		}
+		efc.folderCounts[folder].isImplicit = &isImplicit
+		efc.mu.Unlock()
+	}
+
+	if !isImplicit {
+		glog.V(4).Infof("EmptyFolderCleaner: folder %s is not marked as implicit, skipping", folder)
+		return
+	}
+
+	// Check if folder is actually empty (count up to maxCountCheck)
 	count, err := efc.countItems(ctx, folder)
 	if err != nil {
 		glog.V(2).Infof("EmptyFolderCleaner: error counting items in %s: %v", folder, err)
diff --git a/weed/filer/filer.go b/weed/filer/filer.go
index b3114d112..1b6cbe769 100644
--- a/weed/filer/filer.go
+++ b/weed/filer/filer.go
@@ -9,6 +9,7 @@ import (
 	"strings"
 	"time"
 
+	"github.com/seaweedfs/seaweedfs/weed/s3api/s3_constants"
 	"github.com/seaweedfs/seaweedfs/weed/s3api/s3bucket"
 
 	"github.com/seaweedfs/seaweedfs/weed/cluster/lock_manager"
@@ -273,7 +274,8 @@ func (f *Filer) ensureParentDirectoryEntry(ctx context.Context, entry *Entry, di
 
 		// fmt.Printf("dirParts: %v %v %v\n", dirParts[0], dirParts[1], dirParts[2])
 		// dirParts[0] == "" and dirParts[1] == "buckets"
-		if len(dirParts) >= 3 && dirParts[1] == "buckets" {
+		isUnderBuckets := len(dirParts) >= 3 && dirParts[1] == "buckets"
+		if isUnderBuckets {
 			if err := s3bucket.VerifyS3BucketName(dirParts[2]); err != nil {
 				return fmt.Errorf("invalid bucket name %s: %v", dirParts[2], err)
 			}
@@ -299,6 +301,13 @@ func (f *Filer) ensureParentDirectoryEntry(ctx context.Context, entry *Entry, di
 				GroupNames: entry.GroupNames,
 			},
 		}
+		// level > 3 corresponds to a path depth greater than "/buckets/<bucket_name>",
+		// ensuring we only mark subdirectories within a bucket as implicit.
+		if isUnderBuckets && level > 3 {
+			dirEntry.Extended = map[string][]byte{
+				s3_constants.ExtS3ImplicitDir: []byte("true"),
+			}
+		}
 
 		glog.V(2).InfofCtx(ctx, "create directory: %s %v", dirPath, dirEntry.Mode)
 		mkdirErr := f.Store.InsertEntry(ctx, dirEntry)
@@ -521,3 +530,14 @@ func (f *Filer) Shutdown() {
 	f.LocalMetaLogBuffer.ShutdownLogBuffer()
 	f.Store.Shutdown()
 }
+
+func (f *Filer) GetEntryAttributes(ctx context.Context, p util.FullPath) (map[string][]byte, error) {
+	entry, err := f.FindEntry(ctx, p)
+	if err != nil {
+		return nil, err
+	}
+	if entry == nil {
+		return nil, nil
+	}
+	return entry.Extended, nil
+}
diff --git a/weed/s3api/s3_constants/extend_key.go b/weed/s3api/s3_constants/extend_key.go
index 56f2ac1ea..b4c030d49 100644
--- a/weed/s3api/s3_constants/extend_key.go
+++ b/weed/s3api/s3_constants/extend_key.go
@@ -11,6 +11,7 @@ const (
 	ExtETagKey                  = "Seaweed-X-Amz-ETag"
 	ExtLatestVersionIdKey       = "Seaweed-X-Amz-Latest-Version-Id"
 	ExtLatestVersionFileNameKey = "Seaweed-X-Amz-Latest-Version-File-Name"
+	ExtS3ImplicitDir            = "Seaweed-X-Amz-Implicit-Dir"
 	// Cached list metadata in .versions directory for single-scan efficiency
 	ExtLatestVersionSizeKey        = "Seaweed-X-Amz-Latest-Version-Size"
 	ExtLatestVersionETagKey        = "Seaweed-X-Amz-Latest-Version-ETag"