The photovoltaic (PV) arrays of solar-powered UAVs exhibit typical distributed characteristics, which is of great significance for the efficient and stable management of distributed energy systems. To improve the energy utilization efficiency of PV arrays on the wing, this paper designs a distributed energy management system and proposes a distributed multi-loop energy management with adaptive droop control method. The incremental conductivity (INC) algorithm is applied in the maximum power point tracking (MPPT) control loop to achieve the maximum efficiency output of PV arrays. An adaptive droop control method is proposed for voltage control loop to achieve precise DC bus voltage regulation, current sharing, and power coordination distribution. Simulation results indicate that the proposed multi-loop energy management control method can achieve power distribution and MPPT control for distributed PV arrays, enhancing system stability and reliability, and improving energy utilization efficiency. Semi-physical experimental results indicate that the proposed adaptive droop control method enhances controllability of the distributed energy system and maintains high-precision current sharing and power distribution. Taking flight power demand of the “Dandelion II-C” solar-powered UAV as an example, the proposed multi-loop energy management control method can meet the UAV’s power demand, while ensuring that the PV arrays operate at maximum power point during high power demand phases, and maintain high-efficient operation during low power demand phases. The research results provide a theoretical foundation and engineering support for high-efficiency control of distributed energy systems for solar-powered UAVs.