diff --git a/CHANGELOG.md b/CHANGELOG.md
index bb29daf7ff..0235f027c8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,7 @@ We use *breaking :warning:* word for marking changes that are not backward compa
 
 * [#3095](https://github.com/thanos-io/thanos/pull/3095) Rule: update manager when all rule files are removed.
 * [#3098](https://github.com/thanos-io/thanos/pull/3098) ui: Fix Block Viewer for Compactor and Store
+* [#3105](https://github.com/thanos-io/thanos/pull/3105) Query: Fix overwriting maxSourceResolution when auto downsampling is enabled.
 
 ---
 sse_config:
diff --git a/pkg/api/query/v1.go b/pkg/api/query/v1.go
index 7cc30675b2..6cf2b80496 100644
--- a/pkg/api/query/v1.go
+++ b/pkg/api/query/v1.go
@@ -195,7 +195,8 @@ func (qapi *QueryAPI) parseDownsamplingParamMillis(r *http.Request, defaultVal t
 	val := r.FormValue(maxSourceResolutionParam)
 	if qapi.enableAutodownsampling || (val == "auto") {
 		maxSourceResolution = defaultVal
-	} else if val != "" {
+	}
+	if val != "" && val != "auto" {
 		var err error
 		maxSourceResolution, err = parseDuration(val)
 		if err != nil {
diff --git a/pkg/api/query/v1_test.go b/pkg/api/query/v1_test.go
index 05a91dcc15..bec886d622 100644
--- a/pkg/api/query/v1_test.go
+++ b/pkg/api/query/v1_test.go
@@ -1040,6 +1040,14 @@ func TestParseDownsamplingParamMillis(t *testing.T) {
 			result:                   int64((1 * time.Hour) / 6),
 			fail:                     true,
 		},
+		// maxSourceResolution param can be overwritten.
+		{
+			maxSourceResolutionParam: "1m",
+			enableAutodownsampling:   true,
+			step:                     time.Hour,
+			result:                   int64(time.Minute / (1000 * 1000)),
+			fail:                     false,
+		},
 	}
 
 	for i, test := range tests {