The invention discloses a turning on-off control method of a fuel cell system. The control method comprises a turning on preheating control method. The turning on preheating control method comprises the following steps: 1) in a process of starting a fuel cell, while an indicating temperature is lower than a setting temperature value, closing a contactor by a controller, enabling an electric current generated by a fuel cell stack to flow through a resistance to generate heat, heating cooling water in an internal circulating water route, and warming the fuel cell stack through internal circulation; 2) collecting a real-time current signal of the resistance; 3) according to an expected loading current signal and the real-time current signal, calculating a duty ratio controlled quantity by using PID closed-cycle control through the controller; 4) according to the duty ratio controlled quantity, outputting a PWM signal through the controller, controlling an opening-closing state of an electronic switch, and adjusting a current size of the resistance; and 5) while the indicating temperature is equal to or higher than the setting temperature value, breaking the contactor through the controller. The control method is capable of consuming a surplus reaction gas in the stack during shutdown, and avoiding lifetime decay of the fuel cell caused by overpotential.