The plateau lake basins of Inner Mongolia are important water conservation areas in northern China. They can provide a variety of ecosystem functions such as flood prevention and drought resistance, climate regulation, and biodiversity maintenance. Global climate change and human activities in recent years have led to a significant reduction in the number and area of lakes on the Inner Mongolia Plateau. They are increasingly damaging the ecosystem of plateau lakes and their basins, which has seriously threatened the ecological security of surrounding areas and impeded the ecological construction across the nation. Protection and management of lake basins on the Inner Mongolia Plateau have gradually become a concern and urgent problem to be solved by all sectors of society. With the purpose of improving and enhancing the ecological environment quality and ecosystem functions of the basin, this paper takes the Lake Dalinor basin on the Inner Mongolia Plateau as the research object. Based on the ecological characteristics of the basin and the main ecological environmental issues, three indicators of soil loss, soil erosion and land desertification sensitivity are chosen to evaluate the ecosystem sensitivity of the basin. The importance of the basin ecosystem function is evaluated from three aspects of water conservation, soil conservation and the importance of habitat quality. On this basis, the basin is divided into extremely important-sensitive areas, general important-sensitive areas, and low important-sensitive areas through GIS. Taking the ecosystem importance of the Dalinor National Nature Reserve in the basin into consideration and the results of three regional evaluations, the basin is divided into four areas, namely prohibited zone, key protection zone, quality improvement zone and potential threat zone. The protection measures of the basin are proposed according to each region's ecological characteristics. This research results provide a scientific basis for improving the ecological environment quality of lake basins in plateau areas and implementing scientific and effective management of the basins. At the same time, it has important theoretical and practical significance in promoting regional and global ecological construction and sustainable development.