The Ebinur Lake Basin, a key ecological security barrier for windbreak and sand control in northern Xinjiang, is crucial to the ecological safety of western China and the northern sand-prevention belt. Combining the basin's geographical characteristics, this study comprehensively evaluated ecosystem service functions from four dimensions: water conservation, soil and water conservation, windbreak and sand-fixation, and biodiversity maintenance. Simultaneously, it conducted an ecological sensitivity assessment from four aspects: soil erosion, desertification, land use, and salinization sensitivity. The assessments of the importance of ecosystem service function and ecological sensitivity results were combined to create a tiered zoning plan for the basin. The basin was divided into four first-level zones: the Ebinur Lake Water Area and Wetland Biodiversity Protection Zone, the Desert Vegetation Windbreak and Sand Fixation Ecological Restoration Zone, the Oasis Agricultural Ecological Function Protection Zone, and the Mountain Water Conservation Zone. Six second-level zones were also delineated: the Ebinur Lake Wetland National Nature Reserve, Gobi Vegetation Distribution and Soil Erosion Sensitive Zone, Desert Vegetation Restoration Zone, Jinghe-Bortala Valley Oasis Agricultural Ecological Function Zone, Mountain Water Conservation and Forest-Grass Protection Zone, and Sayram Lake Water Body. This assessment and zoning plan provide support and scientific basis for the basin's comprehensive ecological management, integrated protection and governance of mountains, rivers, forests, farmlands, lakes, grasslands and deserts, as well as regional ecological development.