A fuel cell system and an operation method thereof are provided, which are capable of properly executing special shutdown of the fuel cell system in the event of a trouble in purge operation by use of material gas. In the fuel cell system (100), if an abnormality occurs in a purge process by use of material gas during shutdown of the fuel cell system (100), the controller (11) brings, according to the contents of the abnormality, the opening/closing state of fuel electrode opening/closing devices (26, 23, 24) for opening and closing the outlet/inlet of a fuel electrode (13a), oxidant electrode opening/closing devices (25, 28, 20, 27) for opening and closing the outlet/inlet of an oxidant electrode (13c) or hydrogen generator opening/closing devices (21, 23, 22) for opening and closing the outlet/inlet of a hydrogen generator (12) into a state that is different from their opening/closing state when the purge process by use of the material gas is performed.