Due to high-intensity agricultural production activities and the excessive use of chemical substances such as fertilizers and pesticides, agricultural nonpoint source pollution has surpassed industrial and urban residential pollution to become the number one contributor to nonpoint source pollution in China. Promoting farmers' participation in agricultural nonpoint source pollution management is a key link to achieve the goal of sustainable agricultural development. Based on an expanded theory of planned behavior, we identified the key influencing factors of farmers' participation in agricultural nonpoint source pollution management. According to microsurvey data from 600 farmers in Huai'an, China, we used a structural equation model to analyze in depth the influence of farmers' internal cognition and their perceptions of the external environment to explore the formation mechanism of their participation in agricultural nonpoint source pollution management behavior. The study shows that, first, government regulations promote the green development of the agricultural market environment and social organizations and that farmers' perceptions of the external environment strengthen the influence of their internal cognition but are not fully significant. Second, farmers' internal cognition can enhance their willingness to participate, and the influence of attitudes is the strongest. Finally, there is a positive relationship between the level of response of farmers' participation in pollution control behavior and their perceived behavioral control and willingness to control. Based on the above analysis, we propose policy recommendations in terms of government regulation, market regulation, organization construction, and multisubject collaboration to mobilize the enthusiasm of various subjects and to improve the efficiency of agricultural nonpoint source pollution management. •Application of polycentric governance theory in nonpoint source pollution control.•Government regulations promote the green development of the agricultural environment.•Among farmers' cognition, attitude has the strongest influence on intention.•Farmers' perceptions of the external environment will influence their cognition.•Farmers' perceived behavior control and intention promote their governance behaviors.