A control apparatus for a built-on machine tool according to the invention has a plurality of heads or cutters connected to control axes of respective control systems which are controlled independently by individual control programs. The apparatus includes commander for synchronously issuing a standby command or standby-cancellation command to each system, and timing setting means for setting standby command timing or standby-cancellation command timing between systems brought into coincidence by the command means, wherein standby timing or standby-cancellation timing set with regard to the program of one specific system decides the timing of standby control by the program of another specific system. As a result, a system to be put on standby and a system to be released from standby can be designated at will to enable highly efficient control of the machine tool.