A motor control system is provided for compensating disturbance. The system includes a controller that supplies an input voltage to a motor based on the difference between a current command value to a motor and an actual current of the motor. A motor modeling part outputs a motor output current based on an input voltage from the controller and a disturbance observation part is formed as a reverse model of the motor modeling part to remove current noise using a current differentiation filtering method. Additionally, a disturbance compensation amount determination part determines a disturbance compensation amount based on the disturbance estimated by the disturbance observation part.