Agricultural non-point source pollution is of importance in river deterioration. Thus identifying and concentrated controlling the key source-areas are the most effective approaches for non-point source pollution control. This study adopts inventory method to analysis four kinds of pollution sources and their emissions intensity of the chemical oxygen demand (COD), total nitrogen (TN), and total phosphorus (TP) in 173 counties (cities, districts) in Huaihe River Basin. The four pollution sources include livestock breeding, rural life, farmland cultivation, aquacultures. The paper mainly addresses identification of non-point polluted sensitivity areas, key pollution sources and its spatial distribution characteristics through cluster, sensitivity evaluation and spatial analysis. A geographic information system (GIS) and SPSS were used to carry out this study. The results show that: the COD, TN and TP emissions of agricultural non-point sources were 206.74 x 10(4) t, 66.49 x 10(4) t, 8.74 x 10(4) t separately in Huaihe River Basin in 2009; the emission intensity were 7.69, 2.47, 0.32 t.hm-2; the proportions of COD, TN, TP emissions were 73%, 24%, 3%. The paper achieves that: the major pollution source of COD, TN and TP was livestock breeding and rural life; the sensitivity areas and priority pollution control areas among the river basin of non-point source pollution are some sub-basins of the upper branches in Huaihe River, such as Shahe River, Yinghe River, Beiru River, Jialu River and Qingyi River; livestock breeding is the key pollution source in the priority pollution control areas. Finally, the paper concludes that pollution type of rural life has the highest pollution contribution rate, while comprehensive pollution is one type which is hard to control.