diff --git a/apps/desktop/src/components/diff/SchemaDiffConfigStep.vue b/apps/desktop/src/components/diff/SchemaDiffConfigStep.vue
index 6946109c2d..129fafa971 100644
--- a/apps/desktop/src/components/diff/SchemaDiffConfigStep.vue
+++ b/apps/desktop/src/components/diff/SchemaDiffConfigStep.vue
@@ -448,28 +448,6 @@ async function fetchDbVersion(connectionId: string, database: string, schema: st
           />
         </div>
 
-        <!-- Source Table Selection -->
-        <div class="mt-3 space-y-1.5">
-          <div class="flex items-center justify-between gap-2">
-            <Label class="text-xs font-medium">{{ t("diff.tableSelection") }}</Label>
-            <Button v-if="restrictTables || canConfigureTableSelection" variant="ghost" size="sm" class="h-6 px-2 text-xs" @click="handleToggleRestrict(!restrictTables)">
-              {{ restrictTables ? t("diff.compareAllTables") : t("diff.chooseTables") }}
-            </Button>
-          </div>
-          <div v-if="!restrictTables" class="text-[11px] text-muted-foreground">
-            {{ t("diff.tableSelectionUnrestricted") }}
-          </div>
-          <TableMultiSelect
-            v-if="restrictTables && canConfigureTableSelection"
-            :key="`${sourceConnectionId}.${sourceDatabase}.${sourceSchema}`"
-            :model-value="localSelectedTables"
-            @update:model-value="handleUpdateSelectedTables"
-            :tables="sourceTableList"
-            :title="t('diff.sourceTables')"
-            :empty-text="t('dataCompare.noTables')"
-          />
-        </div>
-
         <!-- Source Info -->
         <div v-if="getConnectionInfo(sourceConnectionId)" class="mt-4 p-3 rounded-lg bg-muted/30 border space-y-1.5">
           <div class="text-xs font-medium text-blue-500">{{ t("diff.info") }}</div>
@@ -555,17 +533,6 @@ async function fetchDbVersion(connectionId: string, database: string, schema: st
           />
         </div>
 
-        <!-- Target Same-Name Match -->
-        <div v-if="restrictTables && localSelectedTables.length && canConfigureTableSelection && isTableIdentityReady('target')" class="mt-3 space-y-1.5 rounded-lg border p-3 text-xs">
-          <div class="font-medium">{{ t("diff.autoMatchHint") }}</div>
-          <div class="text-muted-foreground">
-            {{ t("diff.matchedTables", { matched: matchResult.matched.length, total: localSelectedTables.length }) }}
-          </div>
-          <div v-if="missingTargetTables.length" class="text-destructive">
-            {{ t("diff.missingTargetTables", { tables: missingTargetTables.join(", ") }) }}
-          </div>
-        </div>
-
         <!-- Target Info -->
         <div v-if="getConnectionInfo(targetConnectionId)" class="mt-4 p-3 rounded-lg bg-muted/30 border space-y-1.5">
           <div class="text-xs font-medium text-green-500">{{ t("diff.info") }}</div>
@@ -585,6 +552,41 @@ async function fetchDbVersion(connectionId: string, database: string, schema: st
       </div>
     </div>
 
+    <!-- Comparison Scope -->
+    <div class="space-y-3 rounded-lg border bg-muted/20 p-3">
+      <div class="space-y-1.5">
+        <div class="flex items-center justify-between gap-2">
+          <Label class="text-xs font-medium">{{ t("diff.tableSelection") }}</Label>
+          <Button v-if="restrictTables || canConfigureTableSelection" variant="ghost" size="sm" class="h-6 px-2 text-xs" @click="handleToggleRestrict(!restrictTables)">
+            {{ restrictTables ? t("diff.compareAllTables") : t("diff.chooseTables") }}
+          </Button>
+        </div>
+        <div v-if="!restrictTables" class="text-[11px] text-muted-foreground">
+          {{ t("diff.tableSelectionUnrestricted") }}
+        </div>
+        <TableMultiSelect
+          v-if="restrictTables && canConfigureTableSelection"
+          :key="`${sourceConnectionId}.${sourceDatabase}.${sourceSchema}`"
+          :model-value="localSelectedTables"
+          @update:model-value="handleUpdateSelectedTables"
+          :tables="sourceTableList"
+          :title="t('diff.sourceTables')"
+          :empty-text="t('dataCompare.noTables')"
+        />
+      </div>
+
+      <!-- Target Same-Name Match -->
+      <div v-if="restrictTables && localSelectedTables.length && canConfigureTableSelection && isTableIdentityReady('target')" class="space-y-1.5 rounded-lg border p-3 text-xs">
+        <div class="font-medium">{{ t("diff.autoMatchHint") }}</div>
+        <div class="text-muted-foreground">
+          {{ t("diff.matchedTables", { matched: matchResult.matched.length, total: localSelectedTables.length }) }}
+        </div>
+        <div v-if="missingTargetTables.length" class="text-destructive">
+          {{ t("diff.missingTargetTables", { tables: missingTargetTables.join(", ") }) }}
+        </div>
+      </div>
+    </div>
+
     <!-- Options -->
     <div class="flex items-center gap-2 p-3 rounded-lg border bg-muted/20">
       <input id="schema-diff-ignore-comments" :checked="ignoreComments" type="checkbox" class="accent-primary" @change="$emit('update:ignoreComments', ($event.target as HTMLInputElement).checked)" />
diff --git a/apps/desktop/src/components/diff/__tests__/SchemaDiffDialog.spec.ts b/apps/desktop/src/components/diff/__tests__/SchemaDiffDialog.spec.ts
index 16ba33f997..2cd2c8753c 100644
--- a/apps/desktop/src/components/diff/__tests__/SchemaDiffDialog.spec.ts
+++ b/apps/desktop/src/components/diff/__tests__/SchemaDiffDialog.spec.ts
@@ -54,4 +54,21 @@ describe("SchemaDiffDialog fullscreen layout", () => {
     expect(configStepSource).toContain('v-if="restrictTables && canConfigureTableSelection"');
     expect(configStepSource).toContain("restrictTables && localSelectedTables.length && canConfigureTableSelection && isTableIdentityReady('target')");
   });
+
+  it("keeps explicit table selection in a shared scope below both sides", () => {
+    const comparisonScope = configStepSource.indexOf("<!-- Comparison Scope -->");
+    const targetInfo = configStepSource.indexOf("<!-- Target Info -->");
+    const options = configStepSource.indexOf("<!-- Options -->");
+    const tableSelectors = configStepSource.match(/<TableMultiSelect\b/g) ?? [];
+    const tableSelector = configStepSource.indexOf("<TableMultiSelect", comparisonScope);
+    const targetMatch = configStepSource.indexOf("<!-- Target Same-Name Match -->", comparisonScope);
+
+    expect(comparisonScope).toBeGreaterThan(targetInfo);
+    expect(comparisonScope).toBeLessThan(options);
+    expect(tableSelectors).toHaveLength(1);
+    expect(tableSelector).toBeGreaterThan(comparisonScope);
+    expect(tableSelector).toBeLessThan(options);
+    expect(targetMatch).toBeGreaterThan(comparisonScope);
+    expect(targetMatch).toBeLessThan(options);
+  });
 });