This study presents a hierarchical control strategy for an auxiliary power unit (APU) for aircraft to coordinate multiple power sources and control developed power electronic interfaces. The study benefits from the presence of a hybrid energy system in paralleled structure to the main generator as the complementary system. The employed structure enhances power quality and improves the voltage profile of the high-voltage DC bus. Furthermore, the developed bi-directional topology provides the possibility of interaction with the grid. Considering the APU features in an aircraft, a hierarchical control strategy with different levels of control, timescale, dynamic response, and significance are developed. The developed controller consists of a power management algorithm in the higher level, and local voltage and current controllers in the lower one. The algorithm aims to maximise the PV subsystem utilisation, overcome voltage fluctuations, increase power density, reduce operation costs, and increase system availability while allowing further development to larger systems. Simulation and experimental results confirm the robustness of the algorithm. The result shows that the proposed power sharing strategy optimises the system utilisation while achieving a high-quality voltage profile under severe fluctuations. Moreover, the stress on the battery pack is reduced to improve the life cycle and reduce operation costs.