In this paper, a high-efficiency double DC-DC conversion system is developed for a fuel cell/battery hybrid power propulsion system (HPPS) in long cruising range underwater vehicles. To improve the energy conversion efficiency from the proton exchange membrane fuel cell (PEMFC) to the battery, the operating characteristic of the PEMFC is first studied. Then, two types of DC-DC converters are integrated as the double DC-DC conversion system. The major DC-DC converter can assure high DC- DC conversion efficiency for the majority of the PEMFC output power, while the auxiliary DC-DC converter can track the maximum power point of the PEMFC. In addition, the auxiliary DC-DC converter also focuses on reducing the DC-DC energy losses when the PEMFC works with the standby power. Furthermore, the hysteresis control and the maximum power point tracking control methods are designed for the PEMFC/battery HPPS to implement the power distribution between the PEMFC and the battery. Analyses and validation are done based on a PEMFC/battery HPPS simulation platform and a load profile of an actual underwater vehicle. Compared with the single DC-DC conversion system, the double DC-DC conversion system can better match the operating modes and the output power of the PEMFC. For the long cruising range underwater vehicle at the full cruising range, the overall DC-DC conversion efficiency of the PEMFC/battery HPPS can be improved by about 2.49%.