In the 1980s, China began to recognize the gravity of the problem of non-point agricultural source pollution and conduct research on it. Agricultural non-point source pollution in China, on the other hand, differs from foreign agricultural non-point source pollution and industrial point source pollution. Because the features of agricultural non-point source pollution are complicated, it is critical to investigate a whole-chain management policy system appropriate for China’s agricultural pattern. Based on the current situation of agricultural non-point source pollution in China, this study summarizes the four stages of agricultural non-point source pollution prevention and control policies, namely the discovery stage with macro policies as the main focus, the exploration stage with single research indicators, the initial systematic strengthening stage, and the focused stage with targeted characteristics. Simultaneously, it examined the technological approaches that are suitable for China’s national circumstances and have been investigated by relying on international experience in present-day Chinese management. However, there are still some problems and challenges in agricultural non-point source pollution management policies, such as a lack of non-point source information support, a lack of coordination between different departments, a lack of support in measurement and retroactive calculation and treatment, a lack of an in-depth concept of zoning and classification, a lack of policy, an institutional system, and insufficient capital investment. Based on these problems and combining them with Green Agriculture, Beautiful China, and other goals, this paper puts forward suggestions to strengthen the policy data support of the agricultural non-point source pollution management system, enhance the research and development of the law of pollutant migration and transformation, encourage the innovation of low-cost and high-benefit treatment technology, improve the construction of the management system, strengthen the collaboration of departments, increase the investment of funds, and make other suggestions so as to promote the treatment of agricultural non-point source pollution with high quality and efficiency.