diff --git a/sql/core/src/main/scala/org/apache/spark/sql/execution/basicOperators.scala b/sql/core/src/main/scala/org/apache/spark/sql/execution/basicOperators.scala
index a6a14df6a33ea..fb1c6182cf956 100644
--- a/sql/core/src/main/scala/org/apache/spark/sql/execution/basicOperators.scala
+++ b/sql/core/src/main/scala/org/apache/spark/sql/execution/basicOperators.scala
@@ -79,12 +79,12 @@ case class Filter(condition: Expression, child: SparkPlan)
 
   // Split out all the IsNotNulls from condition.
   private val (notNullPreds, otherPreds) = splitConjunctivePredicates(condition).partition {
-    case IsNotNull(a) if child.output.exists(_.semanticEquals(a)) => true
+    case IsNotNull(a: NullIntolerant) if a.references.subsetOf(child.outputSet) => true
     case _ => false
   }
 
   // The columns that will filtered out by `IsNotNull` could be considered as not nullable.
-  private val notNullAttributes = notNullPreds.flatMap(_.references)
+  private val notNullAttributes = notNullPreds.flatMap(_.references).distinct.map(_.exprId)
 
   // Mark this as empty. We'll evaluate the input during doConsume(). We don't want to evaluate
   // all the variables at the beginning to take advantage of short circuiting.
@@ -92,7 +92,7 @@ case class Filter(condition: Expression, child: SparkPlan)
 
   override def output: Seq[Attribute] = {
     child.output.map { a =>
-      if (a.nullable && notNullAttributes.exists(_.semanticEquals(a))) {
+      if (a.nullable && notNullAttributes.contains(a.exprId)) {
         a.withNullability(false)
       } else {
         a
@@ -179,7 +179,7 @@ case class Filter(condition: Expression, child: SparkPlan)
     // Reset the isNull to false for the not-null columns, then the followed operators could
     // generate better code (remove dead branches).
     val resultVars = input.zipWithIndex.map { case (ev, i) =>
-      if (notNullAttributes.exists(_.semanticEquals(child.output(i)))) {
+      if (notNullAttributes.contains(child.output(i).exprId)) {
         ev.isNull = "false"
       }
       ev