The present invention relates to a wheel alignment apparatus using a motor-driven power steering (MDPS) and a control method thereof. After a vehicle having the MDPS mounted therein is parked, a steering angle is detected and a wheel is aligned with the center by controlling an MDPS motor through a motor angular velocity and a motor current. Accordingly, the motor angular velocity of the MDPS motor which is actually driven to align the wheel with the center is controlled to improve the precision of motor control, regardless of external disturbance such as tire frictions or loads.