An apparatus for controlling an MDPS system including: an autonomous driving cancellation determination unit configured to determine whether to cancel autonomous driving, using column torque passed through a band stop filter, under an autonomous driving condition; and a signal processing unit configured to calculate command steering angle acceleration information using command steering angle information outputted from an autonomous driving system. When the steering angle acceleration information is equal to or greater than a predetermined reference value, the autonomous driving cancellation determination unit may determine that urgent steering is performed by the autonomous driving system, and forbid cancellation of the autonomous driving.