An apparatus for controlling an motor-driven power steering (MDPS) may include: a driving information input unit configured to receive driving information; a steering angle position control unit configured to receive a command steering angle and a current motor steering angle of a driving motor, and output an autonomous driving command; and an MDPS control unit configured to drive the driving motor based on the autonomous driving command in an autonomous driving mode, determine whether a driver intervenes in steering, calculate a driver command by the driver's steering according to whether the driver intervenes in steering, and change an operation mode from the autonomous driving mode to a driver mode while driving the driving motor with a compensation output between the driver command and the autonomous driving command.