diff --git a/flint-spark-integration/src/main/scala/org/opensearch/flint/spark/skipping/ApplyFlintSparkSkippingIndex.scala b/flint-spark-integration/src/main/scala/org/opensearch/flint/spark/skipping/ApplyFlintSparkSkippingIndex.scala
index eee5999ef..a9ebbb8dd 100644
--- a/flint-spark-integration/src/main/scala/org/opensearch/flint/spark/skipping/ApplyFlintSparkSkippingIndex.scala
+++ b/flint-spark-integration/src/main/scala/org/opensearch/flint/spark/skipping/ApplyFlintSparkSkippingIndex.scala
@@ -9,6 +9,7 @@ import org.opensearch.flint.spark.FlintSpark
 import org.opensearch.flint.spark.FlintSparkIndexUtils.isConjunction
 import org.opensearch.flint.spark.skipping.FlintSparkSkippingIndex.{getSkippingIndexName, SKIPPING_INDEX_TYPE}
 
+import org.apache.spark.internal.Logging
 import org.apache.spark.sql.catalyst.catalog.CatalogTable
 import org.apache.spark.sql.catalyst.expressions.{And, Expression, Predicate}
 import org.apache.spark.sql.catalyst.plans.logical.{Filter, LogicalPlan}
@@ -25,7 +26,7 @@ import org.apache.spark.sql.flint.qualifyTableName
  * @param flint
  *   Flint Spark API
  */
-class ApplyFlintSparkSkippingIndex(flint: FlintSpark) extends Rule[LogicalPlan] {
+class ApplyFlintSparkSkippingIndex(flint: FlintSpark) extends Rule[LogicalPlan] with Logging {
 
   override def apply(plan: LogicalPlan): LogicalPlan = plan transform {
     case filter @ Filter( // TODO: abstract pattern match logic for different table support
@@ -36,8 +37,11 @@ class ApplyFlintSparkSkippingIndex(flint: FlintSpark) extends Rule[LogicalPlan]
             Some(table),
             false))
         if isConjunction(condition) && !location.isInstanceOf[FlintSparkSkippingFileIndex] =>
+      logInfo(s"Applying skipping index rewrite rule on filter condition $filter")
       val index = flint.describeIndex(getIndexName(table))
+
       if (index.exists(_.kind == SKIPPING_INDEX_TYPE)) {
+        logInfo(s"Found skipping index $index")
         val skippingIndex = index.get.asInstanceOf[FlintSparkSkippingIndex]
         val indexFilter = rewriteToIndexFilter(skippingIndex, condition)
 
@@ -49,6 +53,7 @@ class ApplyFlintSparkSkippingIndex(flint: FlintSpark) extends Rule[LogicalPlan]
          *        |- FileIndex <== replaced with FlintSkippingFileIndex
          */
         if (indexFilter.isDefined) {
+          logInfo(s"Found filter condition can be pushed down to skipping index: $indexFilter")
           // Enforce hybrid scan if skipping index is partial
           val isHybridScan =
             if (skippingIndex.filterCondition.isDefined) true
@@ -60,9 +65,11 @@ class ApplyFlintSparkSkippingIndex(flint: FlintSpark) extends Rule[LogicalPlan]
           val indexRelation = baseRelation.copy(location = fileIndex)(baseRelation.sparkSession)
           filter.copy(child = relation.copy(relation = indexRelation))
         } else {
+          logInfo("No filter condition can be pushed down to skipping index")
           filter
         }
       } else {
+        logInfo("No skipping index found for query rewrite")
         filter
       }
   }
diff --git a/flint-spark-integration/src/main/scala/org/opensearch/flint/spark/skipping/FlintSparkSkippingFileIndex.scala b/flint-spark-integration/src/main/scala/org/opensearch/flint/spark/skipping/FlintSparkSkippingFileIndex.scala
index b53324f4c..81d2d9d36 100644
--- a/flint-spark-integration/src/main/scala/org/opensearch/flint/spark/skipping/FlintSparkSkippingFileIndex.scala
+++ b/flint-spark-integration/src/main/scala/org/opensearch/flint/spark/skipping/FlintSparkSkippingFileIndex.scala
@@ -8,6 +8,7 @@ package org.opensearch.flint.spark.skipping
 import org.apache.hadoop.fs.{FileStatus, Path}
 import org.opensearch.flint.spark.skipping.FlintSparkSkippingIndex.FILE_PATH_COLUMN
 
+import org.apache.spark.internal.Logging
 import org.apache.spark.sql.{Column, DataFrame}
 import org.apache.spark.sql.catalyst.expressions.Expression
 import org.apache.spark.sql.execution.datasources.{FileIndex, PartitionDirectory}
@@ -28,7 +29,8 @@ case class FlintSparkSkippingFileIndex(
     indexScan: DataFrame,
     indexFilter: Expression,
     isHybridScanMode: Boolean = FlintSparkConf().isHybridScanEnabled)
-    extends FileIndex {
+    extends FileIndex
+    with Logging {
 
   override def listFiles(
       partitionFilters: Seq[Expression],
@@ -42,6 +44,7 @@ case class FlintSparkSkippingFileIndex(
       } else {
         selectFilesFromIndexOnly()
       }
+    logInfo(s"${selectedFiles.size} source files to scan after skipping")
 
     // Keep partition files present in selected file list above
     partitions
@@ -62,21 +65,23 @@ case class FlintSparkSkippingFileIndex(
   /*
    * Left join source partitions and index data to keep unknown source files:
    * Express the logic in SQL:
-   *   SELECT left.file_path
-   *   FROM partitions AS left
-   *   LEFT JOIN indexScan AS right
-   *     ON left.file_path = right.file_path
-   *   WHERE right.file_path IS NULL
-   *     OR [indexFilter]
+   *   SELECT file_path
+   *   FROM partitions
+   *   WHERE file_path NOT IN (
+   *     SELECT file_path
+   *     FROM indexScan
+   *     WHERE NOT [indexFilter]
+   *   )
    */
   private def selectFilesFromIndexAndSource(partitions: Seq[PartitionDirectory]): Set[String] = {
     val sparkSession = indexScan.sparkSession
     import sparkSession.implicits._
 
+    logInfo("Selecting files from both skipping index and source in hybrid scan mode")
     partitions
       .flatMap(_.files.map(f => f.getPath.toUri.toString))
       .toDF(FILE_PATH_COLUMN)
-      .join(indexScan.filter(not(new Column(indexFilter))), Seq(FILE_PATH_COLUMN), "left_anti")
+      .join(indexScan.filter(not(new Column(indexFilter))), Seq(FILE_PATH_COLUMN), "anti")
       .select(FILE_PATH_COLUMN)
       .collect()
       .map(_.getString(0))
@@ -88,6 +93,7 @@ case class FlintSparkSkippingFileIndex(
    * to index store.
    */
   private def selectFilesFromIndexOnly(): Set[String] = {
+    logInfo("Selecting files from skipping index only")
     indexScan
       .filter(new Column(indexFilter))
       .select(FILE_PATH_COLUMN)
diff --git a/integ-test/src/test/scala/org/opensearch/flint/spark/FlintSparkSkippingIndexSqlITSuite.scala b/integ-test/src/test/scala/org/opensearch/flint/spark/FlintSparkSkippingIndexSqlITSuite.scala
index 410def4bc..b119d6008 100644
--- a/integ-test/src/test/scala/org/opensearch/flint/spark/FlintSparkSkippingIndexSqlITSuite.scala
+++ b/integ-test/src/test/scala/org/opensearch/flint/spark/FlintSparkSkippingIndexSqlITSuite.scala
@@ -105,7 +105,7 @@ class FlintSparkSkippingIndexSqlITSuite extends FlintSparkSuite {
              | """.stripMargin)
       sql(s"REFRESH SKIPPING INDEX ON $testTimeSeriesTable")
 
-      // Only 2 rows indexed
+      // Only 1 rows indexed
       flint.describeIndex(testFlintTimeSeriesTable) shouldBe defined
       val indexData = flint.queryIndex(testFlintTimeSeriesTable)
       indexData.count() shouldBe 1