In this paper, a new strategy for modeling and controlling a hybrid power generation system that contains a fuel cell (FC) and super capacitor (SC) system is proposed. The main drawback of FC systems is its slow dynamic because the FC current slope must be limited in order to prevent fuel starvation problems and to improve its efficiency and lifetime. To overcome this slow dynamic and to improve dynamic performance, a new control strategy is proposed to combine FC system with SC system. The proposed control strategy can be also used for cold starting and different types of FC systems with different dynamics. The control strategy is capable of determining the desired FC power to prolong FC system lifetime and keeps the AC and DC voltages around its nominal value in transient event by supplying propulsion power and recuperating FC energy. The minimum SC system is computed in new method and used to meet the load demand to constraint the DC bus voltage and enhances power regulation under various active and reactive load conditions. Two different case studies are used to obtain the simulation results using MATLAB/SIMULINK to verify the validity of the proposed control strategy.