The natural environment and its effectiveness sustained by ecosystem for human life are defined as ecological function or ecological service function. Ecological function regionalization is the basis for understanding the services of ecosystem, evaluating differences and characteristics of eco-system, and identifying countermeasures for resuming degraded ecosystem. Based on the general scheme of ecological regionalization in China, sensitive eco-region of Three Gorges Reservoir Area in Chongqing City was outlined in this study. In this paper, a comprehensive analysis of the ecological environment in Chongqing City was performed and the principals of ecological function regionalization were discussed. Three levels units (physical eco-region, sub-eco-region, and eco-function region) and a comprehensive method of combing quantitative analyses with qualitative analyses were utilized for the regionalization. The main qualitative analyses performed in the regionalization included superimposed graphics and a method of dominant indication; and the quantitative analyses in the regionalization included cluster and principal component analyses. Taking geomorphologic factors as main indexes, physical eco-regions were divided by the cluster analysis and the superimposed graphics. Factors forming features of ecosystem and influencing ecological service function were selected as indexes; sub-eco-regions were divided by the cluster and principal component analyses. To assess the ecological sensitivity and the importance of ecological service function, eco-function regions were divided by the method of dominant indication. Intelligent determination, statistical analysis, and geographical information system (GIS) were taken into account to determine boundary lines of delineation. The results showed that Chongqing Municipality could be ecological characterized as 4 first-level unit areas (physical eco-region), 7 second-level areas (sub-eco-region) and 13 third-level areas (eco-function region).