The invention provides a cooling system of an equipment compartment of a deep-sea space station. The cooling system comprises a seawater power generation system, a seawater cooling system and a seawater processing system. According to the cooling system of the equipment compartment of the deep-sea space station provided by the invention, temperature control of the equipment compartment of the deep-sea space station can be guaranteed, high-pressure seawater outside the station can be used to generate electricity so as to improve electric energy reserve in the station, and seawater which enters the station can be prepared into fresh water so as to replenish limited producing and living use water in the station. Therefore, self-supportability of the deep-sea space station can be improved. Sufficient energy supply of the deep-sea space station is scientifically and reliably guaranteed, the deep-sea space station has a strong life supporting system, and more people can be contained to carry out scientific research of long operation time in deep sea.