Abstract: This study explores the integration of hydropower generation and the ecological flow requirement (EFR) of the Yalong River to achieve optimal operation of the cascade hydropower plants in the middle and lower sections of the river. The investigation includes seven hydropower plants. The revised variable monthly flow method (RVMF) is utilized to calculate the minimum, fair, and optimum ecological flow processes for the river’s mainstream. A joint optimization operation model for the middle and lower Yalong River (MLYR) is developed, aiming to maximize cascade power generation. The Strengthen Elitist Genetic Algorithm is employed to solve the optimization model. The findings indicate that (1) as the EFR of the river increases, the power generation and water resource utilization efficiency of the cascade hydropower plants decrease, with Jinping-II experiencing the most significant decline in power generation; (2) implementing joint optimization operation can sustain a higher EFR level while ensuring the normal operation and power generation benefits of the cascade hydropower plants, thereby mitigating the trade-off between hydro energy development and utilization in the basin and the ecological protection of the river.