An ignition coil control system may include a first ignition coil including a primary coil and a secondary coil; a first switch that selectively electrically-connects the primary coil of the first ignition coil; a second ignition coil including a primary coil and a secondary coil; a second switch that selectively electrically-connects the primary coil of the second ignition coil; a pair of electrodes generating spark discharge by a discharge current generated in the first ignition coil and the second ignition coil; and an ignition controller that controls spark discharge of the pair of electrodes by adjusting an amount and a duration of the discharge current of the first ignition coil and the second ignition coil by turning the first switch and the second switch on or off according to a single pulse signal having a constant voltage including different voltages transmitted from an engine control unit (ECU).