Provided are a system for controlling a motor and a method thereof. The system includes: a data storage unit in which data relating to a thermal equivalent circuit of the motor is stored; a temperature measuring unit which measures a temperature of a cooling medium which enters a cooling flow path portion; a rotation speed measuring unit which measures a rotation speed of a rotor; a driving electric current measuring unit which measures a driving electric current of the motor; a permanent magnet temperature estimating unit which estimates a temperature of the permanent magnet portion of the rotor; and a driving controller controls driving of the motor.