Hydrogen refueling stations (HRSs) will proliferate in the near future as they are prerequisites for the fast developing hydrogen-powered vehicles. The electric-hydrogen hybrid refueling stations based on DC microgrid is a promising way. The HRSs can utilize renewable energy to generate and store hydrogen on site locally. DC bus voltage stability and reliable operation become significant control issues of HRSs based on DC microgrid. In order to solve the problem of power allocation and coordinated operation of lithium battery energy storage system (BESS) and hydrogen energy storage system (HESS), a fuzzy power allocation strategy and control method is proposed for islanding DC microgrid with electric-hydrogen hybrid energy storage system. The operation modes of DC microgrid are analyzed, the fuzzy logic controller (FLC) is designed, and the control methods of different interface converters are given under different operating modes. Finally, simulation model and hardware-in-the loop experimental platform based on RT-LAB are built, the proposed algorithm and traditional method are carried out in simulation model and experimental platform. The simulation and experimental results show that the proposed method can use the fuzzy logic controller to dynamically adjust the allocation factors according to the state-of-charge (SOC) of battery and state-of-charge (SOCH) of hydrogen storage tank, so that the SOC and SOCH gradually tend to a reasonable working range, improve the service life of the battery and hydrogen safety, and reduce the number of control mode switching.