This paper presents the design, development and flight testing of a hydrogen fuel cell (FC) powered quadrotor, where a novel online identification and energy management scheme is implemented and studied. Using a hybrid energy source consisting of a 3 kW proton exchange membrane fuel cell and an auxiliary lithium-ion battery, the unmanned aerial vehicle (UAV) could serve as an aerial operating platform with 3 kg load-carrying capability and achieve an endurance of over 50 minutes. The aircraft design and subsystem structure are summarized, with particular focus on safety. In addition, a novel energy management framework based on online identification is proposed to optimize the FC performance in terms of output power. Employing a particle filter, the nonlinear semi-empirical fuel cell model is updated online according to the dynamic flight condition. Then, key fuel cell characteristics including maximum power point (MPP) and maximum efficiency point (MEP) are extracted from the identified model, and the energy source is regulated by a dynamic energy management strategy to track the optimal operating point of the fuel cell. Outdoor flights were conducted to validate the aircraft design, and superior performance of the proposed energy management strategy against conventional strategies is demonstrated using real flight data.