In recent years, new energy sources such as the hydrogen fuel cell have attracted considerable attention. This paper presents a hydrogen fuel cell power generation system controlled by a virtual synchronous generator. First, the mathematical model of a hydrogen fuel cell is established, and its voltage output characteristics and power characteristics are analyzed. On this basis, a two-stage converter-type grid connected control system is designed. In the control of a virtual synchronous generator, in order to solve the problem that the low frequency characteristic of the first-order filter in the power outer loop affects the stability and dynamic performance of the system, a notch filter is introduced to optimize the compensation based on the original filter. Finally, Matlab/Simulink is used to simulate and compare the filter effect before and after optimization, and the simulation test of side voltage and THD is carried out. This shows the validity and feasibility of the optimized filter and control system. This work is supported by National Natural Science Foundation of China (No. 51767015) and Natural Science Foundation of Gansu Province (No. 2016GS07210).