The performance of the battery used in the traditional solar photovoltaic power generation system is poor, and the solar energy has a certain volatility, which makes the performance of the solar photovoltaic power generation system decline significantly. In order to improve the performance of the solar photovoltaic power generation system, a solar photovoltaic fuel cell combined power generation system has been developed. However, there are some problems in the process of traditional combined generation system optimal scheduling, such as high investment cost and total cost, and short generation time of optimal scheduling scheme. This paper takes solving the problems of traditional system optimal scheduling as the research goal, a new optimization scheduling method of solar photovoltaic and fuel cell combined power generation system was designed. The composition and topological structure of the solar photovoltaic fuel cell combined power generation system are analyzed. The system is composed of photovoltaic array, fuel cell, electrolytic cell, short-term energy storage unit and energy control unit. It can mainly convert sunlight radiation into electric energy, and convert it into DC or AC used by people through multiple links, so as to ensure the stability and security of power supply in our country. A scheduling model is established according to the photovoltaic cell power generation model, the fuel cell power generation model, the electrolytic hydrogen production model, the battery model, the power conversion model and the combined power generation system model. And the multi-objective cuckoo algorithm is used to solve the model, the optimization scheduling results of solar photovoltaic fuel cell combined power generation system are obtained. The experimental results show that the total investment cost of this method is reduced by 123678.4 yuan and 175858.7 yuan compared with the experimental comparison method, and the total cost is reduced by 301195.5 yuan and 414991.8 yuan compared with the experimental comparison method. It shows that compared with the experimental comparison method, the total investment cost and total cost of this method are lower, and the generation time of the optimal scheduling scheme is between 0.19s and 0.25s, and the practical application effect is good. It fully solves the problems existing in the traditional methods and has certain application significance.