Non-point source (NPS) pollution has been increasingly serious in China since the 1990s. The increases of agricultural NPS pollution in China is evaluated for the period 2000-2008 by surveying the literature on water and soil pollution from fertilizers and pesticides, and assessing the surplus nitrogen balance within provinces. The main causes for NPS pollution were excessive inputs of nitrogen fertilizer and pesticides, which were partly the result of the inadequate agricultural extension services and the rapid expansion of intensive livestock production with little of waste management. The annual application of synthetic nitrogen fertilizers and pesticides in China increased by 50.7 and 119.7%, respectively, during 1991-2008. The mitigation measures to reduce NPS pollution include: correct distortion in fertilizer prices; improve incentives for the recycling of organic manure; provide farmers with better information on the sound use of agro-chemicals; and tighten the regulations and national standards on organic waste disposal and pesticides use.