Abstract: Agricultural non-point source pollution is one of the most pressing global environmental challenges, and its formation is a comprehensive and complex process, in which agricultural production activity is a significant influencing factor. From the perspective of biological control in plant protection, and centered on the "4R" strategy for the prevention and control of agricultural non-point source pollution, this paper combines the increasingly prominent issue of agricultural non-point source pollution in China driven by the unscientific and irrational use of chemical fertilizers, pesticides, and agricultural plastic films, synthesizes the fundamental theories, prevention technologies, and practical applications of microorganisms in managing agricultural non-point source pollution induced by these factors, revealing that microorganisms constitute a key pathway for green prevention and control of agricultural non-point source pollution and possess substantial practical potential. This work aims to provide a scientific foundation for further in-depth research and effective mitigation of Agricultural non-point source pollution, while offering both theoretical and practical support for sustainable agricultural development and ecological security.