In this paper, we analyze the current submarine cooling system and study control algorithms for cooling system. Cooling system are installed in the submarine propulsion motor to protect the motor from high-temperature by iron loss and copper loss. The cooling system control the sea water and fresh water pump RPM to keep the motor temperature stable by external environment and motor RPM holding time. The cooling system simulation program is made for checking the cooling performance, and simulation is performed with various control strategy. The results with proposed cooling algorithm is shown to improve the thermal stability and efficiency of cooling system.