Abstract: In order to explore the comprehensive ecological environment of Bosten Lake basin, based on the water quality and water quantity biological data of Bosten Lake and Kaidu River of 2000—2018, this paper used fuzzy evaluation mathematical model to evaluate the current water system situation of the basin, analyzed the water quantity of Bosten Lake and Kaidu River, and preliminarily proposed the optimal control method of water system. The results showed that the water flow of the Kaidu River and the water level of the Bosten Lake in 2000—2018 showed a trend of decreasing first and then increasing. After 2014, the water volume of the Bosten Lake Basin began to surplus; the degree of ecological water demand in Bosten Lake Basin was poor on the whole, showing a tendency of gradual recovery after deterioration. Aiming at the status quo of the water system connection of the Bosten Lake, the basic regulation methods of the Bosten Lake water system with increasing path, in-situ strengthening and node regulation were proposed. The water demand regulation could meet the ecological water demand of the Bosten Lake and increase the ecological water supply of the Peacock River. The scientific combination of the three control methods provided better protection for the water quality of the Bosten Lake, and the industrial, agricultural and domestic water supply of downstream of the Peacock River.