PV system is affected by the natural environment, so its output power is random. Then we need configure a certain capacity of storage devices in order to ensure the supply reliable and continuous. The flywheel energy storage system is an ideal energy storage element. It has high power density. Its speed of charging or discharging is fast. And it is environment-friendly. This paper studies the flywheel energy storage system applying to the Stand-alone Photovoltaic System and respectively analyses the control strategy of the charging/ discharging. In the end, the effectiveness and flexibility of the control strategy is verified by Matlab simulation. The stability of the DC bus voltage is effectively regulated.