Considering the energy supply-demand of solar-powered unmanned aerial vehicles for long-distance flight, this paper investigates the storage balance control problem of the energy system. By taking each power generation in the vehicles as an agent, which is composed of photovoltaic cells, a storage system, and a power output unit, distributed control protocols based on the multi-agent theory are designed to achieve the state-of-charge balance of the energy storage unit, and a corresponded algorithm is proposed to satisfy the constraints of the system. Distributed control protocols are designed for continuous models and discrete models, respectively, and theoretical analysis shows that both the control protocols can achieve our objective. The effectiveness of the proposed control protocols is verified in the semi-physical platform, where the photovoltaic simulator and electronic load are used to establish the operational environment of the energy system, and the 18650 lithium-ion batteries are chosen as the storage unit. The results show that the proposed protocols can effectively solve the unbalance problem caused by the difference of photovoltaic power and battery parameters, and consequently improve the depth of charging/discharging.