China has adopted renewable portfolio standards and tradable green certificates (including hydropower) to increase the proportion of green power used and reduce carbon emissions. However, hydropower generation is affected by seasonal factors, making it difficult to increase green power consumption in water-scarce areas. Trading electricity and green certificates in regions with different resource endowments can effectively solve this problem. Therefore, this study uses evolutionary game theory to explore the impact of the change in the policy of issuing green certificates for hydropower on the strategic choices of the trading parties. Based on the evolutionary game model, a system dynamics model is established to explore the optimization strategies of green power and certificate trading under the influence of seasonal factors. The results of the case study show that (1) the price of green certificates varies with seasonal changes. (2) Sellers with abundant hydropower resources should increase the amount of hydropower connected to the grid during the water-abundant period to help deficit areas achieve their consumption targets (3) Expanding the scope of green certificates can gradually eliminate government subsidies and incentives and reduce the government's financial pressure.