A LLC resonant three port DC-DC converter with integrated photovoltaic and storage design and its advanced control strategy were proposed, for the application requirements of solar powered UAV’s energy manager. Firstly, time-domain analysis was used to analyze the multiple operating modes of the resonant tank of the three-port converter under different power transmission modes. Phase shift control was used to achieve the flexible power control among the three ports. Secondly, polynomial approximation was used to fit the gain surface obtained from time-domain analysis to obtain an accurate mathematical expression for the gain characteristics of the converter. On this basis, a decoupling control strategy was proposed. The design of the decoupling loop could effectively reduce the power coupling degree between multiple control loops of the three-port converter and optimize its dynamic performance. Finally, a 500 W experimental prototype was built, to verify the steady-state operating characteristics, dynamic mode switching process, and decoupling loop design of the three-port topology. The experimental results verified that the time-domain analysis method could accurately describe the circuit characteristics, and the decoupling loop could effectively reduce the degree of power coupling between control loops and improve the dynamic response performance of the system.