diff --git a/internal/unionstore/memdb_test.go b/internal/unionstore/memdb_test.go
index 6003059ae..4f1def3e8 100644
--- a/internal/unionstore/memdb_test.go
+++ b/internal/unionstore/memdb_test.go
@@ -1231,7 +1231,7 @@ func testMemBufferCache(t *testing.T, buffer MemBuffer) {
 }
 
 func TestMemDBLeafFragmentation(t *testing.T) {
-	// RBT cannot pass the leaf fragmentation test.
+	testMemDBLeafFragmentation(t, newRbtDBWithContext())
 	testMemDBLeafFragmentation(t, newArtDBWithContext())
 }
 
diff --git a/internal/unionstore/rbt/rbt.go b/internal/unionstore/rbt/rbt.go
index 06884fb42..a0bce51db 100644
--- a/internal/unionstore/rbt/rbt.go
+++ b/internal/unionstore/rbt/rbt.go
@@ -120,10 +120,12 @@ func (db *RBT) RevertVAddr(hdr *arena.MemdbVlogHdr) {
 		// If there are no flags associated with this key, we need to delete this node.
 		keptFlags := node.getKeyFlags().AndPersistent()
 		if keptFlags == 0 {
-			db.deleteNode(node)
+			node.markDelete()
+			db.count--
+			db.size -= int(node.klen)
 		} else {
-			node.setKeyFlags(keptFlags)
 			db.dirty = true
+			node.resetKeyFlags(keptFlags)
 		}
 	} else {
 		db.size += len(db.vlog.GetValue(hdr.OldValue))
@@ -279,7 +281,7 @@ func (db *RBT) SelectValueHistory(key []byte, predicate func(value []byte) bool)
 // GetFlags returns the latest flags associated with key.
 func (db *RBT) GetFlags(key []byte) (kv.KeyFlags, error) {
 	x := db.traverse(key, false)
-	if x.isNull() {
+	if x.isNull() || x.isDeleted() {
 		return 0, tikverr.ErrNotExist
 	}
 	return x.getKeyFlags(), nil
@@ -347,17 +349,22 @@ func (db *RBT) Set(key []byte, value []byte, ops ...kv.FlagsOp) error {
 	// the NeedConstraintCheckInPrewrite flag is temporary,
 	// every write to the node removes the flag unless it's explicitly set.
 	// This set must be in the latest stage so no special processing is needed.
-	var flags kv.KeyFlags
+	flags := x.GetKeyFlags()
+	if flags == 0 && x.vptr.IsNull() && x.isDeleted() {
+		x.unmarkDelete()
+		db.count++
+		db.size += int(x.klen)
+	}
 	if value != nil {
-		flags = kv.ApplyFlagsOps(x.getKeyFlags(), append([]kv.FlagsOp{kv.DelNeedConstraintCheckInPrewrite}, ops...)...)
+		flags = kv.ApplyFlagsOps(flags, append([]kv.FlagsOp{kv.DelNeedConstraintCheckInPrewrite}, ops...)...)
 	} else {
 		// an UpdateFlag operation, do not delete the NeedConstraintCheckInPrewrite flag.
-		flags = kv.ApplyFlagsOps(x.getKeyFlags(), ops...)
+		flags = kv.ApplyFlagsOps(flags, ops...)
 	}
 	if flags.AndPersistent() != 0 {
 		db.dirty = true
 	}
-	x.setKeyFlags(flags)
+	x.resetKeyFlags(flags)
 
 	if value == nil {
 		return nil
@@ -881,8 +888,11 @@ func (n *memdbNode) getKey() []byte {
 
 const (
 	// bit 1 => red, bit 0 => black
-	nodeColorBit  uint16 = 0x8000
-	nodeFlagsMask        = ^nodeColorBit
+	nodeColorBit uint16 = 0x8000
+	// bit 1 => node is deleted, bit 0 => node is not deleted
+	// This flag is used to mark a node as deleted, so that we can reuse the node to avoid memory leak.
+	deleteFlag    uint16 = 1 << 14
+	nodeFlagsMask        = ^(nodeColorBit | deleteFlag)
 )
 
 func (n *memdbNode) GetKeyFlags() kv.KeyFlags {
@@ -893,10 +903,22 @@ func (n *memdbNode) getKeyFlags() kv.KeyFlags {
 	return kv.KeyFlags(n.flags & nodeFlagsMask)
 }
 
-func (n *memdbNode) setKeyFlags(f kv.KeyFlags) {
+func (n *memdbNode) resetKeyFlags(f kv.KeyFlags) {
 	n.flags = (^nodeFlagsMask & n.flags) | uint16(f)
 }
 
+func (n *memdbNode) markDelete() {
+	n.flags = (nodeColorBit & n.flags) | deleteFlag
+}
+
+func (n *memdbNode) unmarkDelete() {
+	n.flags &= ^deleteFlag
+}
+
+func (n *memdbNode) isDeleted() bool {
+	return n.flags&deleteFlag != 0
+}
+
 // RemoveFromBuffer removes a record from the mem buffer. It should be only used for test.
 func (db *RBT) RemoveFromBuffer(key []byte) {
 	x := db.traverse(key, false)
diff --git a/internal/unionstore/rbt/rbt_iterator.go b/internal/unionstore/rbt/rbt_iterator.go
index dea270b4f..95beeba2c 100644
--- a/internal/unionstore/rbt/rbt_iterator.go
+++ b/internal/unionstore/rbt/rbt_iterator.go
@@ -119,7 +119,7 @@ func (i *RBTIterator) init() {
 		}
 	}
 
-	if i.isFlagsOnly() && !i.includeFlags {
+	if (i.isFlagsOnly() && !i.includeFlags) || (!i.curr.isNull() && i.curr.isDeleted()) {
 		err := i.Next()
 		_ = err // memdbIterator will never fail
 	}
@@ -142,7 +142,7 @@ func (i *RBTIterator) Flags() kv.KeyFlags {
 func (i *RBTIterator) UpdateFlags(ops ...kv.FlagsOp) {
 	origin := i.curr.getKeyFlags()
 	n := kv.ApplyFlagsOps(origin, ops...)
-	i.curr.setKeyFlags(n)
+	i.curr.resetKeyFlags(n)
 }
 
 // HasValue returns false if it is flags only.
@@ -174,6 +174,10 @@ func (i *RBTIterator) Next() error {
 			i.curr = i.db.successor(i.curr)
 		}
 
+		if i.curr.isDeleted() {
+			continue
+		}
+
 		// We need to skip persistent flags only nodes.
 		if i.includeFlags || !i.isFlagsOnly() {
 			break
@@ -195,6 +199,9 @@ func (i *RBTIterator) seekToFirst() {
 	}
 
 	i.curr = y
+	for !i.curr.isNull() && i.curr.isDeleted() {
+		i.curr = i.db.successor(i.curr)
+	}
 }
 
 func (i *RBTIterator) seekToLast() {
@@ -207,6 +214,9 @@ func (i *RBTIterator) seekToLast() {
 	}
 
 	i.curr = y
+	for !i.curr.isNull() && i.curr.isDeleted() {
+		i.curr = i.db.predecessor(i.curr)
+	}
 }
 
 func (i *RBTIterator) seek(key []byte) {