Yunlong Reservoir is the water source project of Zhangjiu River Diversion and Water Supply Project. In order to meet the water demand of Kunming City, Yunlong Reservoir intercepts and stores a large amount of runoff water, which makes it difficult to meet the ecological water demand of the downstream river channel and the hydrological situation has changed seriously. This paper explores how to reduce the impact of reservoirs on the original hydrological situation of downstream rivers and weaken the damage to the ecological environment through reservoir operation under the condition of ensuring the normal water supply of reservoirs. Firstly, this paper improves the RVA method and establishes a multi-objective ecological scheduling model based on the improved RVA method. Then, the NSGA-II algorithm built in the EMO platform is used to solve the joint operation of Shuanghua reservoir and Yunlong reservoir in the Yunlong reservoir basin for five consecutive years. A set of schemes with the lowest degree of economic benefit, social water demand and hydrological change is obtained, and the Tennant method is used to evaluate the ecological flow superiority of the obtained schemes. The results show that the discharge of each reservoir basically meets the basic ecological water demand through ecological scheduling, which verifies the rationality of the model. Finally, in view of the current situation of the reservoir, this paper puts forward suggestions on improving the water supply of Yunlong Reservoir and improving the compensation ability of ecological water.