diff --git a/statistics/cmsketch.go b/statistics/cmsketch.go
index 31abbbc6dc458..4335e90d82b62 100644
--- a/statistics/cmsketch.go
+++ b/statistics/cmsketch.go
@@ -799,10 +799,7 @@ func MergePartTopN2GlobalTopN(loc *time.Location, version int, topNs []*TopN, n
 	if checkEmptyTopNs(topNs) {
 		return nil, nil, hists, nil
 	}
-
 	partNum := len(topNs)
-	removeVals := make([][]TopNMeta, partNum)
-
 	// Different TopN structures may hold the same value, we have to merge them.
 	counter := make(map[hack.MutableString]float64)
 	// datumMap is used to store the mapping from the string type to datum type.
@@ -864,22 +861,11 @@ func MergePartTopN2GlobalTopN(loc *time.Location, version int, topNs []*TopN, n
 				if count != 0 {
 					counter[encodedVal] += count
 					// Remove the value corresponding to encodedVal from the histogram.
-					removeVals[j] = append(removeVals[j], TopNMeta{Encoded: datum.GetBytes(), Count: uint64(count)})
+					hists[j].BinarySearchRemoveVal(TopNMeta{Encoded: datum.GetBytes(), Count: uint64(count)})
 				}
 			}
 		}
 	}
-	// Remove the value from the Hists.
-	for i := 0; i < partNum; i++ {
-		if len(removeVals[i]) > 0 {
-			tmp := removeVals[i]
-			slices.SortFunc(tmp, func(i, j TopNMeta) bool {
-				cmpResult := bytes.Compare(i.Encoded, j.Encoded)
-				return cmpResult < 0
-			})
-			hists[i].RemoveVals(tmp)
-		}
-	}
 	numTop := len(counter)
 	if numTop == 0 {
 		return nil, nil, hists, nil
diff --git a/statistics/histogram.go b/statistics/histogram.go
index d4f7e9ed72447..642836c83a941 100644
--- a/statistics/histogram.go
+++ b/statistics/histogram.go
@@ -281,6 +281,35 @@ func (hg *Histogram) BucketToString(bktID, idxCols int) string {
 	return fmt.Sprintf("num: %d lower_bound: %s upper_bound: %s repeats: %d ndv: %d", hg.bucketCount(bktID), lowerVal, upperVal, hg.Buckets[bktID].Repeat, hg.Buckets[bktID].NDV)
 }
 
+// BinarySearchRemoveVal removes the value from the TopN using binary search.
+func (hg *Histogram) BinarySearchRemoveVal(valCntPairs TopNMeta) {
+	lowIdx, highIdx := 0, hg.Len()-1
+	for lowIdx <= highIdx {
+		midIdx := (lowIdx + highIdx) / 2
+		cmpResult := bytes.Compare(hg.Bounds.Column(0).GetRaw(midIdx*2), valCntPairs.Encoded)
+		if cmpResult > 0 {
+			lowIdx = midIdx + 1
+			continue
+		}
+		cmpResult = bytes.Compare(hg.Bounds.Column(0).GetRaw(midIdx*2+1), valCntPairs.Encoded)
+		if cmpResult < 0 {
+			highIdx = midIdx - 1
+			continue
+		}
+		if hg.Buckets[midIdx].NDV > 0 {
+			hg.Buckets[midIdx].NDV--
+		}
+		if cmpResult == 0 {
+			hg.Buckets[midIdx].Repeat = 0
+		}
+		hg.Buckets[midIdx].Count -= int64(valCntPairs.Count)
+		if hg.Buckets[midIdx].Count < 0 {
+			hg.Buckets[midIdx].Count = 0
+		}
+		break
+	}
+}
+
 // RemoveVals remove the given values from the histogram.
 // This function contains an **ASSUMPTION**: valCntPairs is sorted in ascending order.
 func (hg *Histogram) RemoveVals(valCntPairs []TopNMeta) {