A combination of multiple power sources, known as a hybrid energy system (HES), has been considered to increase flight time for unmanned aerial vehicle applications. Two separated or combined converters, which can be defined as a fully active hybrid converter, can be placed between power sources and the load to manage energy flows from sources. This paper proposed a novel digital energy management control strategy for fully active hybrid converters, comprised of the mode identification strategy and digital control algorithm, which can realize four crucial functions: 1) regulation of the output voltage, 2) energy management control, 3) charging and discharging operations of battery, and 4) protective control for energy sources. And the control strategy has been validated by both the experiment and simulation based on a hybrid converter prototype, which is designed for 400 W (16.8 V/ 24 A) output and two energy sources, a 500 W fuel cell (FC) and 12 stack Li-Po battery with 39.6-50.4 V voltage range and 44.4 V nominal voltage