A non-uniform displacement engine control system having a transient state control mode includes a non-uniform displacement engine including a plurality of cylinders, the cylinders including 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 unit for controlling the motor, wherein the motor control unit controls the motor such that a sum of engine torque and motor torque in explosion strokes of each cylinder is uniform by compensating for a difference in torque caused by the cylinders having different displacements, and the motor control unit has a transient state control mode for additionally applying offset torque to predetermined motor torque at a time of rapid acceleration or rapid deceleration.