System and method of controlling ignition timing in an engine with a variably operated intake valve

A system and method of optimally controlling ignition timings in an engine conditioned in first and second modes of intake control. A control unit includes an unthrottled operation control conducting the first mode by varying a closing timing of an intake valve and fixing a throttle position of a throttle valve, a throttled operation control conducting the second mode by varying the throttle position of the throttle valve and fixing the closing timing of the intake valve, and an ignition timing control determining different ignition timings to be used in the first and second modes.