The aquatic ecological function regionalization is the basic requirement of water resources management, water environment protection and water ecology restoration. Especially for lake basins which are connected closely with human activities and filled with inconsistencies, the aquatic ecological function regionalization is an indispensable condition of realizing sustainable development in the watershed. So how to delineate reasonable ecological function regionalization becomes the major issue to be addressed in the integrated watershed management. In the case of Lake Dianchi basin, the dominant water ecological functions are first determined according to the current problems of water ecosystems. And in the premise of hydrological integrity, sub-catchment units are divided for the first and the second level regionalization respectively. Then we indentify the key factors that affect water ecological function significantly and construct the index system for the watershed based on the relative theories, including ecosystem service function, scale effect and rule of territorial differentiation. The overlaying and clustering methods are used for multiple indices. Then final boundary is adjusted slightly according to water quantity and quality distribution. The consequence shows that Lake Dianchi basin is divided into 5 level Ⅰecological function regions and 10 level Ⅱecological function regions. By using the density of periphytic algae and Limnodrilus, assessment is made on the reasonability of regionalization. Finally the problems remained in the water ecological function regionalization are discussed.