Owing to rapid development of power device and inverters, most of submarines adopt an eletric propulsion system. Although PMPM(Permanent Magnet Propulsion Motor) propulsion system has relatively higher power, energy conversion efficiency and smaller volume than engine propulsion system, it also produces large amount of heat due to current flowing inside motor coils and change of magnetic field induced by iron core. The produced heat in stator and inverter largely affects motor efficiency and bearing lubrication and causes thermal aging while the system is on operation. So, we analyze the existing cooling system and submarine ESS (Energy Saving System) cooling system whose power consumption is reduced. HILS(Hardware In the Loop System) technique is used for the modelling of the submarine cooling system. To confirm the ESS cooling system characteristic, HILS is simulated using LabVIEW with hardware. As a result, the ESS cooling system has the characteristic of better temperature stability and less power consumption than the existing one.