An ignition coil control system may include first and second ignition coils, and a spark plug including a pair of electrodes in which generates spark discharge by discharge currents of the first ignition coil and the second ignition coil, a DC-DC converter connected to a primary coil of the first ignition coil, a primary coil of the second ignition coil and a battery; in which converts current magnitude supplied to a primary coil of the first ignition coil and a primary coil of the second ignition coil from a battery, and a controller in which controls the spark discharge of the electrodes by adjusting an amount and a duration of the discharge current of the first ignition coil and the second ignition coil base on a pulse signal, wherein the controller is configured to selectively execute a multi-state ignition through the first ignition coil and the second ignition coil and a single-stage ignition through one of the first ignition coil and the second ignition coil according to an operation region of an engine.