Regionalization exerts an important guiding role for sound environmental management, regional development, and schemes toward regionalizing ecological function, involving multiple levels. This paper formulated a framework for a detailed regionalization approach using the Ashi River watershed, China, as case study. Human activities, especially agriculture non-point source pollution (ANPS) and social factors, were identified as main factors. The results indicated that (1) the export coefficient model (ECM) can be used to determine ANPS loads in the watershed as well as total nitrogen and total phosphorus loads. (2) The minimum cumulative resistance model (MCR) showed that the middle and lower reaches had high risk for ANPS occurrence. (3) Based on the identified key factors, the watershed was divided into level IV and combined with existing level III using cluster analysis. Corresponding management countermeasures were proposed. This provides a scientific basis for pollution control planning and for management measures.