For the hybrid energy storage system composed of batteries and super capacitors, an energy storage control strategy to smooth photovoltaic output power fluctuations is designed. The low-pass filtering algorithm with threshold judgment is used to design the total charging power of energy storage systems, avoiding the unnecessary regulation to control photovoltaic output power fluctuations. Considering the charging state of energy storage medium, the principle of moving average is used to design the power allocation strategy of storage medium, exerting advantages of different storage medium fully and optimizing the overall performance of hybrid energy storage systems. Simulation analysis verified the validity of the control strategy designed, the energy storage control system can smooth photovoltaic output power fluctuations at the lowest cost. The super-capacitor smoothes the power fluctuations of the fast varying component, reducing the charge number of the storage battery effectively. Research results provide theoretical reference for the application of hybrid energy storage systems in smoothing photovoltaic output power fluctuations.#$NLKeyword: photovoltaic output power; battery; super capacitor; low pass filter; threshold judgment; moving average