Abstract: Hydrogen fuel cell powered aircraft has the advantages of weak infrared characteristics and low operating noise. It can achieve long-endurance and long-distance flight, which is of great significance in military reconnaissance applications. In this paper, a current-fed half-bridge DC/DC converter was adopted to extend the lifespan of PEMFC and solve the voltage mismatch problem between PEMFC and the bus. The model predictive control inner loop controller and feed-forward control outer loop controller were designed to improve the response performance of the system. As the largest power consumption part of PEMFC system, the power consumed by air compressor varied and superimposed with load current. Thus, the extended Kalman observer was designed to estimate the equivalent disturbance of load perturbation and model mismatch caused by inaccurate PEMFC and converter modeling. Then, the prediction model was corrected to improve the ability of rejecting the perturbation. Finally, a 250W experimental prototype was designed to verify the performance of the proposed controller.