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Power flow control strategy is very important for fuel cell (FC) vehicle (FCV) with energy storage (ES) to improve the system dynamic performance and increase system efficiency. The design of power flow strategy will also affect the size of ES and life cycles of FC and ES. Traditionally, power flow control strategies are studied either using hardware power train test bed or using pure software (PC based) simulation. The former method is costly and time consuming. The latter method suffers from lack of accuracy since large simulation time-step has to be adopted because of limited computation capability. This paper presents a new solution to study power flow control strategies for FCV with ES by using real time digital simulator (RTDS). In particular, a proton exchange membrane (PEM) FC system dynamic model and an ultra-capacitor (UC) dynamic model are integrated in the FC vehicle power train to study the power flow control. A unified averaged model of proposed three-phase bidirectional DC-DC converter is developed. Two power flow control strategies of two FCV power trains are proposed. The FCV power trains are simulated in real time on RTDS and two power flow control strategies performances are compared through simulation. The simulation results confirmed that this approach provided a fast, accurate and flexible method for studying FCV power management strategies and performance.