The polymer electrolyte membrane (PEM) fuel cell system is considered to be an ideal alternative for the internal combustion engine, especially when used on a city bus. Hybrid buses with fuel cell systems and energy storage systems are now undergoing transit service demonstrations worldwide. A hybrid PEM fuel cell city bus with a hierarchical control system is studied in this paper. Firstly, the powertrain and hierarchical control structure is introduced. Secondly, the vehicle control strategy including start-stop strategy, energy management strategy, and fuel cell control strategy, including the hydrogen system and air system control strategies, are described in detail. Finally, the performance of the fuel cell was analyzed based on road test data. Results showed that the different subsystems were well-coordinated. Each component functioned in concert in order to ensure that both safety and speed requirements were satisfied. The output current of the fuel cell system changed slowly and the output voltage was limited to a certain range, thereby enhancing durability of the fuel cell. Furthermore, the economic performance was optimized by avoiding low load conditions.