The invention belongs to the field of motor controllers, and provides a power device control and over temperature protection system and a method for a motor controller. Three-phase current is acquired through a current module; three-phase lower bridge arm turn-on voltage is acquired through a voltage module; a first CLARKE/PARK conversion unit acquires d-axis current and q-axis current; a second CLARKE/PARK conversion unit acquires d-axis voltage and q-axis voltage; and a control module acquires the internal resistance of the power device according to the q-axis current and q-axis voltage and obtains the maximum drain-source current of the power device to drive a vector control unit to correspondingly control the working state of the power device. Thus, when the power device is below the conventional working temperature, the output power is increased along with decreasing of the temperature, the current flow ability is made full use of, and the torque output of the motor controller is enhanced; and when the power device is above the conventional working temperature, the output power is decreased along with increasing of the temperature, long-term high temperature operation to damage the power device is prevented, and the damage possibility is reduced.