Under the background of air pollution and sharp decrease of fossil energy reserves, the fuel cell aircraft composed of fuel cell and auxiliary energy storage device has been widely studied due to its characteristics of zero emission and high energy density. In this paper, a system-level mathematical model of fuel cell aircraft is proposed, including kinematics and dynamics aircraft model to achieve the force analysis and motion discription so as to obtain the power demand curve of the whole flight commission. Then, two effective energy management strategies (EMS) based on state machine are designed to improve the system stability and fuel economy. The simulation result proves the EMS can greatly distribute the power demand to the fuel cell and battery rationally to keep the SOC and remained hydrogen in a proper range, which improves the performance of the powertrain and energy economy.