An apparatus for controlling a motor driven power steering (MDPS) system, characterized in that the apparatus comprises: an MDPS basic logic unit configured to determine a first auxiliary command current (I ref_A) for driving an MDPS motor in a manual driving mode of a vehicle on the basis of a column torque applied to a steering column of the vehicle; an autonomous driving steering control unit configured to determine a second auxiliary command current (I ref_B) for driving the MDPS motor in an autonomous driving mode of the vehicle; a filter unit configured to filter the column torque so that noise torque caused by a mechanical mechanism of an MDPS system mounted on the vehicle is removed; and a control unit configured to control whether to activate the filter unit according to whether a predefined sudden steering condition is satisfied, to judge a driver's steering intervention on the basis of selectively filtered column torque according to whether the filter unit is activated, to determine a final auxiliary command current (I ref_final) by applying a weight determined on the basis of the selectively filtered column torque to the first and second auxiliary command currents (I ref_A,I ref_B), and to control switching from the autonomous driving mode to the manual driving mode by driving the MDPS motor through the determined final auxiliary command current (I ref_final), characterized in that the control unit judges the driver's steering intervention by using a variable reference time variably determined corresponding to the selectively filtered column torque, and judges that the driver's steering intervention has occurred when a state in which the selectively filtered column torque is equal to or greater than preset first reference torque is maintained for the variable reference time or longer. an MDPS basic logic unit configured to determine a first auxiliary command current (I ref_A) for driving an MDPS motor in a manual driving mode of a vehicle on the basis of a column torque applied to a steering column of the vehicle; an autonomous driving steering control unit configured to determine a second auxiliary command current (I ref_B) for driving the MDPS motor in an autonomous driving mode of the vehicle; a filter unit configured to filter the column torque so that noise torque caused by a mechanical mechanism of an MDPS system mounted on the vehicle is removed; and a control unit configured to control whether to activate the filter unit according to whether a predefined sudden steering condition is satisfied, to judge a driver's steering intervention on the basis of selectively filtered column torque according to whether the filter unit is activated, to determine a final auxiliary command current (I ref_final) by applying a weight determined on the basis of the selectively filtered column torque to the first and second auxiliary command currents (I ref_A,I ref_B), and to control switching from the autonomous driving mode to the manual driving mode by driving the MDPS motor through the determined final auxiliary command current (I ref_final), characterized in that the control unit judges the driver's steering intervention by using a variable reference time variably determined corresponding to the selectively filtered column torque, and judges that the driver's steering intervention has occurred when a state in which the selectively filtered column torque is equal to or greater than preset first reference torque is maintained for the variable reference time or longer.