The sources of agricultural non-point source pollution in rural water bodies in China are complicated and difficult to control. It is particularly urgent to investigate comprehensive solution of agricultural non-point source pollution issues in terms of production distribution, resource utilization, and the follow-up operation of the treatment projects. Results showed that the pollutant sources in rural waters mainly include five aspects, i.e. fecal and waste water derived from livestock and poultry breeding, aquaculture drainage, cropland drainage, and rural domestic sewage and village surface runoff. According to the characteristics of non-point source pollution in water bodies and the actual situation in rural areas, the strategy of “focusing on prevention and paying equal attention to prevention and control treatment” should be applied. The technique route of comprehensive prevention and control should be determined based on the generation, transport, and fate of pollutants. The technique route includes source reduction, process intercept, end consumption, and resource recycling utilization. Appropriate treatment plan could be determined, which could be summarized as the following: 1) insisting on the overall distribution for comprehensive prevention and control measures in a unit of small watershed or catchment; 2) insisting on applying no-power, low-cost, and ecological control technologies, and 3) insisting on the operation and maintenance mode of agricultural pollutant resource recycling utilization and strengthening follow-up management for treatment projects.