A method of shutting down operation of a fuel cell vehicle includes: blocking, by a controller, an air supply to a fuel cell stack when an operation shutting down command of the fuel cell vehicle is applied; increasing, by the controller, a voltage at an rear end of a stack main relay connected to the fuel cell stack; and opening, by the controller, the stack main relay when the voltage at the rear end of the stack main relay is higher than a stack voltage by a predetermined voltage or more.