set global innodb_file_per_table=1; CREATE TABLE ref_table1 (id int(11) NOT NULL, PRIMARY KEY(id)) ENGINE=InnoDB; CREATE TABLE ref_table2 (id int(11) NOT NULL, PRIMARY KEY(id)) ENGINE=InnoDB; CREATE TABLE `main` ( `id` int(11) NOT NULL AUTO_INCREMENT, `ref_id1` int(11) NOT NULL, `ref_id2` int(11) NOT NULL, PRIMARY KEY (`id`), UNIQUE KEY `idx_1` (`ref_id1`,`ref_id2`), KEY `FK_set_out_analysis_route_id` (`ref_id2`), CONSTRAINT `FK_1` FOREIGN KEY (`ref_id1`) REFERENCES `ref_table1` (`id`) , CONSTRAINT `FK_2` FOREIGN KEY (`ref_id2`) REFERENCES `ref_table2` (`id`) ) ENGINE=InnoDB; SET FOREIGN_KEY_CHECKS=0; DROP INDEX `idx_1` ON `main`; SHOW TABLES; Tables_in_test main ref_table1 ref_table2 # restart ALTER TABLE `main` ADD INDEX `idx_1` (`ref_id1`); SHOW CREATE TABLE `main`; Table Create Table main CREATE TABLE `main` ( `id` int(11) NOT NULL AUTO_INCREMENT, `ref_id1` int(11) NOT NULL, `ref_id2` int(11) NOT NULL, PRIMARY KEY (`id`), KEY `FK_set_out_analysis_route_id` (`ref_id2`), KEY `idx_1` (`ref_id1`), CONSTRAINT `FK_1` FOREIGN KEY (`ref_id1`) REFERENCES `ref_table1` (`id`), CONSTRAINT `FK_2` FOREIGN KEY (`ref_id2`) REFERENCES `ref_table2` (`id`) ) ENGINE=InnoDB DEFAULT CHARSET=latin1 DROP TABLE main, ref_table1, ref_table2;