The contribution of phosphorus and nitrogen from non-point source pollution (NPS) in the Taihu Lake region was investigated through case study and surveying in the town of Xueyan, From experimental results coupled with survey and statistics in the studied area, the distribution of nitrogen and phosphorus input to the water body is achieved from four main sources: agricultural land, village, the town center and the poultry factory. The results showed that about 38% of total phosphorus (TP) and 48% of total nitrogen (TN) discharged is from agricultural land, 33% of TP and 40% TN from village residents, 25% of TP and 10% of TN from the town center and 4% of TP and 2% of TN from the poultry factory. The Agricultural Non-point Pollution Potential Index (APPI) system for identifying and ranking critical areas of NPS was established with a Geographic Information Systems (GIS)-based technology. Quantification of the key factors in non-point sources pollution was carried out utilizing the following: Sediment Production Index (SPI), Runoff Index (RI), People and Animal Loading Index (PALI) and Chemical Use Index (CUI). These are the core parts of the model, and the weighting factor of each index was evaluated according the results of quantification. The model was successfully applied for evaluating APPI in Xueyan. Results from the model showed that the critical area identified for NPS control in Xueyan. The model has several advantages including: requiring fewer parameters, easy acquirement of these parameters, friendly interface, and convenience of operation. In addition it is especially useful for identifying critical areas of NPS when the basic data are not fully accessible, which is the present situation in China.