To address the problem of excessive fluctuation of PV system output power that prevents grid connection, a hybrid energy storage control strategy is introduced to smooth out the fluctuation. For the delay phenomenon of PV output power after smoothing by traditional low-pass filtering algorithm, a low-pass filtering algorithm with variable filtering coefficient is proposed to calculate the target value of output power in real time and set a suitable fluctuation threshold under the boundary of satisfying fluctuation index, so as to reduce the unnecessary regulation of energy storage system. At the same time, the SOC fuzzy control strategy is proposed for the hybrid energy storage system, and the two-stage power command allocation method composed of the low-pass filter for primary allocation and the secondary correction based on the energy storage SOC fuzzy control realizes the reasonable power allocation, which improves the regulation characteristics and operation economy of the hybrid energy storage system while ensuring the safety of the energy storage system.