Provided is an apparatus for operating interior permanent magnet synchronous motor in a system including a detector measuring a position and a speed of a rotor of an IPMSM, the apparatus including an output unit generating and outputting a current command driving a MTPA (Maximum Torque Per Ampere) based on the command torque, a correction unit correcting the current command outputted by the output unit, a feedback unit transmitting over-modulated voltage information to the correction unit, a control unit controlling the current command to output a voltage, a first limit unit limiting an output of the control unit using a maximum voltage synthesizable by an inverter unit, and the inverter unit applying a 3-phase voltage command for tracking a command torque to the IPMSM using an output of the first limit unit.