With the expansion of the scope and diversity of agricultural non-point source (AGNPS) pollution, environmental pollution in water bodies and soils has intensified, seriously affecting the quality of life of urban and rural residents. This paper presents a comprehensive analysis of the current status of AGNPS pollution from five aspects: fertilizers, pesticides, agricultural films, livestock and crop residues. The study also includes a comprehensive risk assessment of the nitrogen and phosphorus pollution, microplastic pollution, and heavy metal contamination attributed to the current AGNPS pollution in China. The findings reveal widespread nitrogen and phosphorus pollution across provinces in China, a low risk of microplastic pollution, and acute contamination with heavy metals such as As, Cd and Hg, notably in Hubei, Gansu, Liaoning, Guizhou, and Hunan. Additionally, the study reveals that in Chinese provinces currently facing severe heavy metal pollution, heavy metal contamination constitutes a significant carcinogenic risk to adult health and a serious non-carcinogenic risk to child health. Consequently, guided by the ‘3R theory’ principles of source reduction, interception, and remediation, this paper suggests an array of expanded strategies for AGNPS pollution management. These strategies are proposed to aid in the sustainable advancement of AGNPS pollution control.