In order to improve the universality of the distributed energy system with fuel cells as the main power supply, a distributed energy system with fuel cells as the main power supply, batteries as auxiliary sources, which can integrate wind and light energy, has been developed. According to the characteristics of the fuel cell, the battery capacity threshold control strategy, the battery charge and discharge current control strategy are proposed. The fuzzy PID equalization algorithm is used to design the automatic control of the fuel cell’s stability and automatic power load track. Based on the proposed control strategy, a set of 4 kW distributed energy power generation system was developed. The results show that the control strategy is practical and effective.