mysql> create table a (id int not null primary key);
Query OK,  0  rows affected ( 0 . 13  sec)

mysql> create table b (id int not null primary key);
Query OK,  0  rows affected ( 0 . 06  sec)

mysql> insert into b VALUES ( 1 ),( 2 ),( 3 );
Query OK,  3  rows affected ( 0 . 02  sec)
Records:  3   Duplicates:  0   Warnings:  0 

mysql> insert into a VALUES ( 1 );
Query OK,  1  row affected ( 0 . 00  sec)

mysql> delete  FROM b_alias USING b b_alias, (SELECT b.id FROM b LEFT JOIN a ON b.id = a.id WHERE a.id IS NULL) a_alias WHERE a_alias.id=b_alias.id;
Query OK,  2  rows affected ( 0 . 00  sec)

mysql> select * from b;
+----+
| id |
+----+
|   1  |
+----+
 1  row in set ( 0 . 00  sec)