Village rules and formal environmental regulations are of great significance for standardizing farmers’ cleaner production behavior, promoting green transformation of agriculture and realizing sustainable development of agriculture. Based on the survey data of 946 farmers in five provinces of China, taking seed coating technology, soil testing and formulated fertilization technology, subsoiling tillage technology, green technology for pest and disease control and straw returning technology as examples, this article empirically analyzes the impact of village rules and formal environmental regulations on farmers’ cleaner production behavior by using the multivariate probit model. When formal environmental regulations are relatively lacking or weak, village rules can be used as a useful supplement to formal environmental regulations to promote farmers’ participation in cleaner production. Based on this, this article argues that the important reason for formal environmental regulations falling into relative system failure is that village rules have not been paid enough attention in promoting farmers’ cleaner production behavior. In the future, we should not only continue to strengthen the role of formal environmental regulations in farmers’ cleaner production, but also cultivate the informal institution represented by the village rules, and build the regulatory system of mutual support between informal institution and formal institution.