With the increasing proportion of new energy in the power grid, it is difficult to meet the high-quality frequency modulation requirements of the power system only relying on traditional thermal power units. This paper proposes a capacity allocation method of the wind-photovoltaic-hydropower-thermal multi-source frequency modulation system based on the stackelberg game theory. Firstly, the thermal power unit is taken as the leader and the wind-photovoltaic-hydropower units are the followers. Secondly, by solving the stackelberg game model, the optimal frequency regulation capacity of each unit participating in frequency regulation is obtained. Then, the improved shapley value method is used to optimize the revenue of the wind-photovoltaic-hydropower units. Finally, the effectiveness of the proposed method is verified. The stackelberg game multi-source frequency modulation model can make the frequency modulation allocation more reasonable and give consideration to the revenue.