The present invention provides a fuel cell pressure balance automatic regulating apparatus and a fuel cell system, wherein the automatic regulating apparatus comprises a shell with a cavity, an upper cover for sealing the shell, and a rotor arranged in the shell; the shell includes a base and a housing in sealing connection with the base; the rotor is arranged at a center region of the base; the rotor includes a rotor body and a first blade for separating the cavity; an inner wall of the housing is provided with a second blade for separating the cavity; the first blade and the second blade separate the cavity into sealing and independent first cavity and second cavity; the rotor body and the first blade are connected and provided with a first gas passage entering the first cavity; and the second blade is provided with a second gas passage entering the second cavity. The fuel cell system can better improve the service life of a membrane cell in the fuel cell and improve the performance of the fuel cell system.