Abstract Against the problem of power fluctuation in the photovoltaic microgrid system, the power fluctuation can be smoothed out by hybrid energy storage technology. Still, the limited capacity of two energy storage units will cause safety problems, such as overcharging and over-discharging in two types of energy storage units and reduce the life of the energy storage device. Therefore, a secondary power distribution control strategy for two types of energy storage units considering dual SOC is proposed. Firstly, the system unbalanced power is calculated. The system unbalanced power is divided through the second-order low-pass filter to obtain the primary distribution power. Then, the SOC of the battery and supercapacitor is divided into nine regions. Finally, the power demand and the SOC in the nine regions are considered simultaneously. Then, the secondary power allocation is carried out for two types of energy storage units. In Matlab/Simulink, the modeling of Photovoltaic microgrids is established, and the simulation results verify the feasibility of the control strategy.