diff --git a/internal/querynodev2/pipeline/filter_node.go b/internal/querynodev2/pipeline/filter_node.go
index 42e02c95be..5fb6f18b30 100644
--- a/internal/querynodev2/pipeline/filter_node.go
+++ b/internal/querynodev2/pipeline/filter_node.go
@@ -30,7 +30,6 @@ import (
 	"github.com/milvus-io/milvus/pkg/util/merr"
 	"github.com/milvus-io/milvus/pkg/util/paramtable"
 	"github.com/milvus-io/milvus/pkg/util/tsoutil"
-	"github.com/milvus-io/milvus/pkg/util/typeutil"
 )
 
 // filterNode filter the invalid message of pipeline
@@ -38,7 +37,7 @@ type filterNode struct {
 	*BaseNode
 	collectionID     UniqueID
 	manager          *DataManager
-	excludedSegments *typeutil.ConcurrentMap[int64, uint64]
+	excludedSegments *ExcludedSegments
 	channel          string
 	InsertMsgPolicys []InsertMsgFilter
 	DeleteMsgPolicys []DeleteMsgFilter
@@ -96,7 +95,9 @@ func (fNode *filterNode) Operate(in Msg) Msg {
 			out.append(msg)
 		}
 	}
-
+	if fNode.excludedSegments.ShouldClean() {
+		fNode.excludedSegments.CleanInvalid(streamMsgPack.EndTs)
+	}
 	metrics.QueryNodeWaitProcessingMsgCount.WithLabelValues(fmt.Sprint(paramtable.GetNodeID()), metrics.InsertLabel).Inc()
 	return out
 }
@@ -133,7 +134,7 @@ func newFilterNode(
 	collectionID int64,
 	channel string,
 	manager *DataManager,
-	excludedSegments *typeutil.ConcurrentMap[int64, uint64],
+	excludedSegments *ExcludedSegments,
 	maxQueueLength int32,
 ) *filterNode {
 	return &filterNode{
diff --git a/internal/querynodev2/pipeline/filter_node_test.go b/internal/querynodev2/pipeline/filter_node_test.go
index 07df419c2d..b25d8d6930 100644
--- a/internal/querynodev2/pipeline/filter_node_test.go
+++ b/internal/querynodev2/pipeline/filter_node_test.go
@@ -18,6 +18,7 @@ package pipeline
 
 import (
 	"testing"
+	"time"
 
 	"github.com/samber/lo"
 	"github.com/stretchr/testify/suite"
@@ -26,7 +27,6 @@ import (
 	"github.com/milvus-io/milvus/internal/querynodev2/segments"
 	"github.com/milvus-io/milvus/pkg/mq/msgstream"
 	"github.com/milvus-io/milvus/pkg/util/paramtable"
-	"github.com/milvus-io/milvus/pkg/util/typeutil"
 )
 
 // test of filter node
@@ -38,7 +38,7 @@ type FilterNodeSuite struct {
 	channel      string
 
 	validSegmentIDs    []int64
-	excludedSegments   *typeutil.ConcurrentMap[int64, uint64]
+	excludedSegments   *ExcludedSegments
 	excludedSegmentIDs []int64
 	insertSegmentIDs   []int64
 	deleteSegmentSum   int
@@ -62,10 +62,12 @@ func (suite *FilterNodeSuite) SetupSuite() {
 	suite.errSegmentID = 7
 
 	// init excludedSegment
-	suite.excludedSegments = typeutil.NewConcurrentMap[int64, uint64]()
+	suite.excludedSegments = NewExcludedSegments(0 * time.Second)
+	excludeInfo := map[int64]uint64{}
 	for _, id := range suite.excludedSegmentIDs {
-		suite.excludedSegments.Insert(id, 1)
+		excludeInfo[id] = 1
 	}
+	suite.excludedSegments.Insert(excludeInfo)
 }
 
 // test filter node with collection load collection
diff --git a/internal/querynodev2/pipeline/filter_policy.go b/internal/querynodev2/pipeline/filter_policy.go
index 3e51bb7577..8e795452a9 100644
--- a/internal/querynodev2/pipeline/filter_policy.go
+++ b/internal/querynodev2/pipeline/filter_policy.go
@@ -18,7 +18,13 @@ package pipeline
 
 import (
 	"fmt"
+	"sync"
+	"time"
 
+	"go.uber.org/atomic"
+	"go.uber.org/zap"
+
+	"github.com/milvus-io/milvus/pkg/log"
 	"github.com/milvus-io/milvus/pkg/util/merr"
 )
 
@@ -54,11 +60,8 @@ func InsertOutOfTarget(n *filterNode, c *Collection, msg *InsertMsg) error {
 }
 
 func InsertExcluded(n *filterNode, c *Collection, msg *InsertMsg) error {
-	ts, ok := n.excludedSegments.Get(msg.SegmentID)
+	ok := n.excludedSegments.Verify(msg.SegmentID, msg.EndTimestamp)
 	if !ok {
-		return nil
-	}
-	if msg.EndTimestamp <= ts {
 		m := fmt.Sprintf("Segment excluded, id: %d", msg.GetSegmentID())
 		return merr.WrapErrSegmentLack(msg.GetSegmentID(), m)
 	}
@@ -88,3 +91,60 @@ func DeleteOutOfTarget(n *filterNode, c *Collection, msg *DeleteMsg) error {
 	// all growing will be be in-memory to support dynamic partition load/release
 	return nil
 }
+
+type ExcludedSegments struct {
+	mu            sync.RWMutex
+	segments      map[int64]uint64 // segmentID -> Excluded TS
+	lastClean     atomic.Time
+	cleanInterval time.Duration
+}
+
+func NewExcludedSegments(cleanInterval time.Duration) *ExcludedSegments {
+	return &ExcludedSegments{
+		segments:      make(map[int64]uint64),
+		cleanInterval: cleanInterval,
+	}
+}
+
+func (s *ExcludedSegments) Insert(excludeInfo map[int64]uint64) {
+	s.mu.Lock()
+	defer s.mu.Unlock()
+
+	for segmentID, ts := range excludeInfo {
+		log.Debug("add exclude info",
+			zap.Int64("segmentID", segmentID),
+			zap.Uint64("ts", ts),
+		)
+		s.segments[segmentID] = ts
+	}
+}
+
+func (s *ExcludedSegments) Verify(segmentID int64, ts uint64) bool {
+	s.mu.RLock()
+	defer s.mu.RUnlock()
+	if excludeTs, ok := s.segments[segmentID]; ok && ts <= excludeTs {
+		return false
+	}
+	return true
+}
+
+func (s *ExcludedSegments) CleanInvalid(ts uint64) {
+	s.mu.Lock()
+	defer s.mu.Unlock()
+
+	invalidExcludedInfos := []int64{}
+	for segmentsID, excludeTs := range s.segments {
+		if excludeTs < ts {
+			invalidExcludedInfos = append(invalidExcludedInfos, segmentsID)
+		}
+	}
+
+	for _, segmentID := range invalidExcludedInfos {
+		delete(s.segments, segmentID)
+	}
+	s.lastClean.Store(time.Now())
+}
+
+func (s *ExcludedSegments) ShouldClean() bool {
+	return time.Since(s.lastClean.Load()) > s.cleanInterval
+}
diff --git a/internal/querynodev2/pipeline/pipeline.go b/internal/querynodev2/pipeline/pipeline.go
index f5332d4d35..995adec414 100644
--- a/internal/querynodev2/pipeline/pipeline.go
+++ b/internal/querynodev2/pipeline/pipeline.go
@@ -17,15 +17,13 @@
 package pipeline
 
 import (
-	"go.uber.org/zap"
+	"time"
 
 	"github.com/milvus-io/milvus/internal/querynodev2/delegator"
 	base "github.com/milvus-io/milvus/internal/util/pipeline"
-	"github.com/milvus-io/milvus/pkg/log"
 	"github.com/milvus-io/milvus/pkg/metrics"
 	"github.com/milvus-io/milvus/pkg/mq/msgdispatcher"
 	"github.com/milvus-io/milvus/pkg/util/paramtable"
-	"github.com/milvus-io/milvus/pkg/util/typeutil"
 )
 
 // pipeline used for querynode
@@ -37,18 +35,12 @@ type Pipeline interface {
 type pipeline struct {
 	base.StreamPipeline
 
-	excludedSegments *typeutil.ConcurrentMap[int64, uint64]
+	excludedSegments *ExcludedSegments
 	collectionID     UniqueID
 }
 
 func (p *pipeline) ExcludedSegments(excludeInfo map[int64]uint64) { //(segInfos ...*datapb.SegmentInfo) {
-	for segmentID, ts := range excludeInfo {
-		log.Debug("pipeline add exclude info",
-			zap.Int64("segmentID", segmentID),
-			zap.Uint64("ts", ts),
-		)
-		p.excludedSegments.Insert(segmentID, ts)
-	}
+	p.excludedSegments.Insert(excludeInfo)
 }
 
 func (p *pipeline) Close() {
@@ -65,7 +57,7 @@ func NewPipeLine(
 	delegator delegator.ShardDelegator,
 ) (Pipeline, error) {
 	pipelineQueueLength := paramtable.Get().QueryNodeCfg.FlowGraphMaxQueueLength.GetAsInt32()
-	excludedSegments := typeutil.NewConcurrentMap[int64, uint64]()
+	excludedSegments := NewExcludedSegments(paramtable.Get().QueryNodeCfg.CleanExcludeSegInterval.GetAsDuration(time.Second))
 
 	p := &pipeline{
 		collectionID:     collectionID,
diff --git a/pkg/util/paramtable/component_param.go b/pkg/util/paramtable/component_param.go
index 63c92abc84..96168e6089 100644
--- a/pkg/util/paramtable/component_param.go
+++ b/pkg/util/paramtable/component_param.go
@@ -1909,9 +1909,6 @@ func (p *queryCoordConfig) init(base *BaseTable) {
 type queryNodeConfig struct {
 	SoPath ParamItem `refreshable:"false"`
 
-	FlowGraphMaxQueueLength ParamItem `refreshable:"false"`
-	FlowGraphMaxParallelism ParamItem `refreshable:"false"`
-
 	// stats
 	// Deprecated: Never used
 	StatsPublishInterval ParamItem `refreshable:"true"`
@@ -1979,6 +1976,11 @@ type queryNodeConfig struct {
 	EnableWorkerSQCostMetrics ParamItem `refreshable:"true"`
 
 	ExprEvalBatchSize ParamItem `refreshable:"false"`
+
+	// pipeline
+	CleanExcludeSegInterval ParamItem `refreshable:"false"`
+	FlowGraphMaxQueueLength ParamItem `refreshable:"false"`
+	FlowGraphMaxParallelism ParamItem `refreshable:"false"`
 }
 
 func (p *queryNodeConfig) init(base *BaseTable) {
@@ -2426,6 +2428,15 @@ Max read concurrency must greater than or equal to 1, and less than or equal to
 	}
 
 	p.ExprEvalBatchSize.Init(base.mgr)
+
+	p.CleanExcludeSegInterval = ParamItem{
+		Key:          "queryCoord.cleanExcludeSegmentInterval",
+		Version:      "2.4.0",
+		DefaultValue: "60",
+		Doc:          "the time duration of clean pipeline exclude segment which used for filter invalid data, in seconds",
+		Export:       true,
+	}
+	p.CleanExcludeSegInterval.Init(base.mgr)
 }
 
 // /////////////////////////////////////////////////////////////////////////////