Aiming at the increasingly widespread application of hydrogen fuel cells in microgrid, this paper relies on the wind/photovoltaic/hydrogen fuel cell DC interconnection system in the hydrogen-power coupled DC microgrid demonstration project in Cixi, Ningbo, to study the port power coordinated control strategy of the three-port DC transformer, which is the core equipment for hydrogen fuel cell access. To shorten the simulation time, a switching period averaging model applicable to a multi-modular series-parallel multi-active bridge structure DC transformer is proposed and adopted in this paper. Moreover, an energy coordination control strategy of the fuel cell-energy storage hybrid supplying system is proposed by applying this equivalent simplified model. The control strategy can optimally adjust the power instructions of each port according to the state of charge （SOC） of energy storage, the power capacity of each port, and the dynamic response speed of the fuel cell. Thus, it can prevent the fuel cell power generation power change too quickly, avoid the overcharges and over-discharges of energy storage, and maximizes the proportion of hydrogen power generation. The simulation results using MATLAB Simulink and experiment waveforms verify that the coordinated control strategy works well in various control modes of the DC transformer. The actual power of the port with power control mode can follow the rapidly changing instruction value, and the actual voltage fluctuation of the port with voltage control mode can be controlled below 4% when the load changes suddenly.