Abstract: After point pollution was effectively controlled, the nonpoint source pollution has become more and more seuere. The increasing nonpoint source pollution has already affected the healthy and benign development of ecology and environment, and even limited the sustained development of China’s economy at a certain extent. In this study, based on the practice of more than 30 years in studying nonpoint source pollution, the total status of agricultural nonpoint source pollution in China was analyzed. Combined with the produce, development and occurrence characterization of agricultural nonpoint source pollution, the strategy for controlling agricultural nonpoint source pollution – “Reduce-retain-restore” theory (3R theory), was proposed according to the economic mode of Chinese agriculture. The 3R theory was explained in this study, and testified using two typical examples of controlling agricultural nonpoint source pollution in Taihu Lake and Dianchi Lake watersheds, respectively. The 3R theory is prospected to provide a valuable guidance for construction of the engineering of controlling agricultural nonpoint source pollution in China or some areas of similar agricultural economic modes.