China’s rural ecological environment presents pollution intertwined state, and the government, enterprises and villagers have different interests and conflicting behavioral motives, which seriously restricts the sustainable development of rural areas. Under the perspective of shared governance, considering villagers as the core governance force and introducing carbon reward and punishment mechanisms, we establish a game model of rural environmental evolution in which village enterprises, local people’s governments and local villagers collaborate in governance, and use numerical simulation to analyze the behavioral strategy choices and stability conditions of each evolutionary game subject. The results of the study show that local people’s governments, village enterprises and villagers have mutual influence and constraints in the joint governance of the rural environment, and a reasonable carbon incentive and penalty mechanism for villagers will eventually achieve the ideal governance mode of tripartite cooperation. Under a reasonable carbon incentive and penalty mechanism, village enterprises and villagers can actively participate in rural environmental governance, and when the intensity of incentives and penalties exceeds a certain “critical value”, their cooperative behaviors will gradually evolve into a stable strategy in which enterprises strictly reduce emissions and villagers actively participate in governance.