diff --git a/sea-orm-cli/src/commands/generate.rs b/sea-orm-cli/src/commands/generate.rs
index a07ca2e38..31e32af1a 100644
--- a/sea-orm-cli/src/commands/generate.rs
+++ b/sea-orm-cli/src/commands/generate.rs
@@ -137,7 +137,10 @@ pub async fn run_generate_command(
                         sqlx_connect::<Sqlite>(max_connections, url.as_str(), None).await?;
                     println!("Discovering schema ...");
                     let schema_discovery = SchemaDiscovery::new(connection);
-                    let schema = schema_discovery.discover().await?;
+                    let schema = schema_discovery
+                        .discover()
+                        .await?
+                        .merge_indexes_into_table();
                     let table_stmts = schema
                         .tables
                         .into_iter()
diff --git a/sea-orm-codegen/src/entity/transformer.rs b/sea-orm-codegen/src/entity/transformer.rs
index ceeb8cf93..c994d9f12 100644
--- a/sea-orm-codegen/src/entity/transformer.rs
+++ b/sea-orm-codegen/src/entity/transformer.rs
@@ -148,6 +148,17 @@ impl EntityTransformer {
                         break;
                     }
                 }
+                if rel.columns.len() == entity.primary_keys.len() {
+                    let mut count_pk = 0;
+                    for primary_key in entity.primary_keys.iter() {
+                        if rel.columns.contains(&primary_key.name) {
+                            count_pk += 1;
+                        }
+                    }
+                    if count_pk == entity.primary_keys.len() {
+                        unique = true;
+                    }
+                }
                 let rel_type = if unique {
                     RelationType::HasOne
                 } else {