NOVELTY - The method involves determining whether an instruction to stop an operation of a fuel cell (20) is detected and an in-stop-mode power generating process in which fuel gas i.e. hydrogen gas, is not supplied and oxide gas i.e. air, is supplied to the cell to generate power that has been executed. Execution time for a diluting process i.e. hydrogen diluting process, is shortened by a scavenging apparatus (15) when the in-stop-mode power generating process has been executed, as compared with a case where the in-stop-mode power generating process has not been executed.    USE - Method for controlling a fuel cell system mounted on a fuel cell vehicle i.e. fuel cell car.    ADVANTAGE - The execution time for the diluting process is shortened by the scavenging apparatus when the in-stop-mode power generating process has been executed, as compared with the case where the in-stop-mode power generating process has not been executed, thus reducing energy loss of the fuel cell system. The method enables shortening the time for generating scavenging gas after power generation of the fuel cell system is stopped by shortening the execution time for the diluting process when the in-stop-mode power generating process has been executed, thus shortening drive time for driving the scavenging apparatus for generating the scavenging gas, and hence reducing energy consumption of the fuel cell system after power generation is stopped. The method enables suppressing a dry state of a cathode to prevent a current-voltage characteristic from dropping at a next activation time, thus reducing fuel consumption of the fuel cell system and power performance of the fuel cell system. The method enables shortening the time for operating the fuel cell system after an operation of the fuel cell system is stopped, thus reducing uncomfortable feeling of a user caused by activation of the fuel cell system for scavenging purpose, and hence improving merchantability of the fuel cell system. The method enables determining of the in-stop-mode power generating process that has been executed without requiring an additional cost by detecting an anode pressure reduced by the in-stop-mode power generating process by using an anode pressure sensor or based on an accumulated current value.    DESCRIPTION OF DRAWING(S) - The drawing shows a schematic block diagram of a fuel cell system.    Fuel cell system (10)    Fuel cell stack (12)    Oxide-gas supply apparatus (14)    Scavenging apparatus (15)    Fuel cell (20)