diff --git a/mvcc/index.go b/mvcc/index.go
index 626de3825fcc..22dec99a11a7 100644
--- a/mvcc/index.go
+++ b/mvcc/index.go
@@ -185,27 +185,32 @@ func (ti *treeIndex) RangeSince(key, end []byte, rev int64) []revision {
 
 func (ti *treeIndex) Compact(rev int64) map[revision]struct{} {
 	available := make(map[revision]struct{})
-	var emptyki []*keyIndex
 	if ti.lg != nil {
 		ti.lg.Info("compact tree index", zap.Int64("revision", rev))
 	} else {
 		plog.Printf("store.index: compact %d", rev)
 	}
-	// TODO: do not hold the lock for long time?
-	// This is probably OK. Compacting 10M keys takes O(10ms).
 	ti.Lock()
-	defer ti.Unlock()
-	ti.tree.Ascend(compactIndex(rev, available, &emptyki))
-	for _, ki := range emptyki {
-		item := ti.tree.Delete(ki)
-		if item == nil {
-			if ti.lg != nil {
-				ti.lg.Panic("failed to delete during compaction")
-			} else {
-				plog.Panic("store.index: unexpected delete failure during compaction")
+	clone := ti.tree.Clone()
+	ti.Unlock()
+
+	clone.Ascend(func(item btree.Item) bool {
+		keyi := item.(*keyIndex)
+		ti.Lock()
+		keyi.compact(rev, available)
+		if keyi.isEmpty() {
+			item := ti.tree.Delete(keyi)
+			if item == nil {
+				if ti.lg != nil {
+					ti.lg.Panic("failed to delete during compaction")
+				} else {
+					plog.Panic("store.index: unexpected delete failure during compaction")
+				}
 			}
 		}
-	}
+		ti.Unlock()
+		return true
+	})
 	return available
 }
 
@@ -222,17 +227,6 @@ func (ti *treeIndex) Keep(rev int64) map[revision]struct{} {
 	return available
 }
 
-func compactIndex(rev int64, available map[revision]struct{}, emptyki *[]*keyIndex) func(i btree.Item) bool {
-	return func(i btree.Item) bool {
-		keyi := i.(*keyIndex)
-		keyi.compact(rev, available)
-		if keyi.isEmpty() {
-			*emptyki = append(*emptyki, keyi)
-		}
-		return true
-	}
-}
-
 func (ti *treeIndex) Equal(bi index) bool {
 	b := bi.(*treeIndex)
 
diff --git a/mvcc/index_bench_test.go b/mvcc/index_bench_test.go
new file mode 100644
index 000000000000..e7120be57c30
--- /dev/null
+++ b/mvcc/index_bench_test.go
@@ -0,0 +1,28 @@
+package mvcc
+
+import (
+	"testing"
+
+  "go.uber.org/zap"
+)
+
+func BenchmarkIndexCompact1(b *testing.B)   { benchmarkIndexCompact(b, 1) }
+func BenchmarkIndexCompact100(b *testing.B) { benchmarkIndexCompact(b, 100) }
+func BenchmarkIndexCompact10000(b *testing.B) { benchmarkIndexCompact(b, 10000) }
+func BenchmarkIndexCompact100000(b *testing.B) { benchmarkIndexCompact(b, 100000) }
+func BenchmarkIndexCompact1000000(b *testing.B) { benchmarkIndexCompact(b, 1000000) }
+
+func benchmarkIndexCompact(b *testing.B, size int) {
+  log := zap.NewNop()
+  kvindex := newTreeIndex(log)
+
+	bytesN := 64
+	keys := createBytesSlice(bytesN, size)
+	for i := 1; i < size; i++ {
+		kvindex.Put(keys[i], revision {main: int64(i), sub: int64(i)})
+	}
+	b.ResetTimer()
+	for i := 1; i < b.N; i++ {
+		kvindex.Compact(int64(i))
+	}
+}
diff --git a/mvcc/kvstore.go b/mvcc/kvstore.go
index f03b6311e4f4..3d941335ea7a 100644
--- a/mvcc/kvstore.go
+++ b/mvcc/kvstore.go
@@ -245,9 +245,10 @@ func (s *store) Compact(rev int64) (<-chan struct{}, error) {
 	// ensure that desired compaction is persisted
 	s.b.ForceCommit()
 
-	keep := s.kvindex.Compact(rev)
 	ch := make(chan struct{})
 	var j = func(ctx context.Context) {
+		keep := s.kvindex.Compact(rev)
+		indexCompactionPauseDurations.Observe(float64(time.Since(start) / time.Millisecond))
 		if ctx.Err() != nil {
 			s.compactBarrier(ctx, ch)
 			return
@@ -261,7 +262,6 @@ func (s *store) Compact(rev int64) (<-chan struct{}, error) {
 
 	s.fifoSched.Schedule(j)
 
-	indexCompactionPauseDurations.Observe(float64(time.Since(start) / time.Millisecond))
 	return ch, nil
 }