A system and method are provided for estimating temperature of a rotor of a motor configured to calculate temperature of the rotor using an actual measured data-based thermal model (thermal impedance model) and an energy loss model, and to estimate temperature of the rotor using the calculated temperature variation of the rotor. The method includes calculating, by a controller, an energy loss of the motor using driving conditions of the motor. The controller is also configured to calculate a temperature variation of the rotor in a predetermined reference temperature using the calculated energy loss and thermal resistances of the rotor and a stator of the motor. Further, the controller is configured to estimate a rotor temperature in the predetermined reference temperature using the temperature variation of the rotor.