A non-uniform displacement engine control system with different control modes based on a state of charge (SOC) of a battery, the system includes a non-uniform displacement engine including a plurality of cylinders, the cylinders comprising at least two sizes of cylinders having different displacements, a motor connected to a driving shaft of the engine, a battery for supplying electrical energy to the motor, and a motor control device for controlling the motor, wherein the motor control device controls the motor to compensate for a difference in torque due to different displacements of the cylinders such that a sum of engine torque and motor torque in explosion stroke of each cylinder is uniform, and the motor control device has a charge intention mode or a discharge intention mode based on the SOC of the battery.