Agricultural non-point source pollution has become the main part of water pollution prevention and control in China. This paper made a brief introduction to the causes and hazards of agricultural non-point source pollution and the current situation of agricultural non-point source pollution prevention and control in China. In view of the serious agricultural non-point source pollution in water environment of Guangxi and the difference in quality of drinking water between urban and rural areas, it came up with recommendations for strengthening agricultural non-point source pollution prevention and control from scientific distribution, linked operation and maintenance, popular science education, and legal system construction, to guarantee safe and healthy drinking water in rural areas.