A stop control method for a fuel cell system of a vehicle can include: determining whether a fuel cell of the fuel cell system is shut down when a key-off signal is received; comparing a voltage of the fuel cell with a first set voltage when it is determined that the fuel cell is not shut down; controlling a voltage of a high-voltage terminal downwardly when the voltage of the fuel cell is larger than the first set voltage; turning on a cathode oxygen depletion (COD) relay a first time after controlling the voltage of the high-voltage terminal downwardly; turning off a high-voltage terminal relay a first time after turning on the COD relay, the high-voltage relay disposed between the fuel cell and the high-voltage terminal; and shutting down the fuel cell and performing key-off control after turning off the high-voltage terminal relay.