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Vehicle controller unit (VCU) plays an important role in fuel cell/battery hybrid vehicles and there is a need to investigate the influence of the embedded algorithm on vehicle performance. An effective way for such an investigation is via a hardware-in-the-loop (HIL) simulation. This paper describes a HIL simulation system that is developed for this purpose. An overview of the system is provided, followed by descriptions of models for vehicle dynamics, electric motor, fuel cell, battery and etc.. The embedded control algorithm contains two parts, the driver command explanation block and the adaptive supervisory control strategy. Results of the HIL simulation system verify the effectiveness of the control algorithm.