Abstract: Agricultural non-point source pollution (AGNPS) incurs certain ecological and environmental risks. After over two decades of governance efforts, substantial progress has been achieved in both the fundamental research and the prevention and control of AGNPS in China. A comprehensive monitoring and evaluation system for the entire process of source and sink paths of AGNPS at the basin, regional or national scale has been established. The primary controlling factors of nitrogen and phosphorus loss within farmland systems under diverse ecological circumstances have been essentially clarified, and the pollution and prevention and control mechanisms of toxic and harmful chemical/biological pollution in farmland have been initially identified. At the technological level of prevention and control, the following have been developed: novel and green fertilizer substitution techniques and products for reducing the input of conventional chemical fertilizers, nitrogen and phosphorus efficient utilization and pollution load reduction technologies, soil nitrogen and phosphorus capacity-increasing and load reduction technologies, nitrogen and phosphorus loss control technologies for sloping farmland, and agricultural waste resource utilization technologies along with digestion equipment. Although the pollution load of agricultural nitrogen and phosphorus emissions in China has demonstrated an overall downward trend, it remains the predominant pollution factor influencing the environmental quality in China. Furthermore, AGNPS exhibits new characteristics, manifested by the increasingly prominent pollution issues in the breeding industry, particularly in the aquaculture sector. The pollution problems associated with new pollutants such as residual plastic film, pesticides, antibiotics, hormones, pathogenic microorganisms, etc. cannot be disregarded. The pathways of AGNPS have shifted from being dominated by runoff diffusion to a stage where leaching, volatilization and accumulation are of equal significance. The pollution medium has transitioned from a single surface water body to a state where underground water bodies, the atmosphere and farmland ecosystems coexist. In the future, grounded on the scientific research accomplishments and relevant information resources attained in this domain in China, digital technology and AI technology should be employed to construct a big data model and system theory integrating prevention and control technologies and management of AGNPS in China. Research on the integration and engineering application of multi-scale AGNPS prevention and control technologies such as farmland plots, basins and regions should be continuously intensified. New quality productivity industries of green and low-carbon agriculture should be cultivated. The guarantee mechanisms and measures of the “government−industry−university−research−application” for prevention and control technology projects should be implemented to enhance the comprehensive environmental, economic and social benefits of AGNPS prevention and control technologies at the regional or basin scale, thereby comprehensively advancing the governance of AGNPS in China and facilitating the high-quality and healthy development of agriculture.