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The main tributaries of the upper reaches of the Yangtze River are not only the strategic base for China’s water resources, but also an important hydropower base for the “West-East Power Transmission Strategy”. With the completion of these reservoir groups, a large-scale mixed reservoir system across the different basins has been formed, which makes the requirements for joint optimization and scheduling of large-scale hydropower system getting higher and higher. This paper focuses on the key problems faced by the joint optimization of large-scale hydropower system in the basin. Taking the Yalong River and the middle and downstream of the Jinsha River as the research area, the hybrid optimization method is introduced herein to solve the joint optimal scheduling model. The results reveal that the power generation by joint optimal scheduling is much more than separately scheduling, and the total power generation increased by 2.84% on average. As Mid-Jinsha cascade and Yalong River cascade has a 690 million kW·h and 190 million kW·h decrease in power generation respectively, the downstream Jinsha River cascade has a power generation increase of 4.31 billion kW·h.