According a method of protecting a motor-driven power steering system from overheat, it is possible to prevent a steering motor and an ECU from being broken by overheat by controlling electric current supplied to the steering motor, by calculating an engine stop time from radiation temperature maps stored in a memory and changes in temperature of a temperature sensor when the engine having been stopped restarts without operating a specific protection logic when the engine stops, and calculating temperature of the steering motor and the ECU from the radiation temperature maps and the engine stop time.