The PPP mode of rural water environment governance was conducive to attracting social capital for giving full play to the decisive role of the market in resource allocation, coordinating the interests of all parties, and relieving the government budget pressure and debt burden. The cooperation strategy of rural water environment governance PPP projects was analyzed from the perspective of evolutionary game, and dynamic process between project company and farmers was elaborated. First, evolutionary game theory was applied to study the cooperation strategy selection between stakeholders, i.e., the project company and farmers in PPP mode of rural water environment governance project, and evolutionary game model and duplicate dynamic equation were presented for cooperation with project company and farmers, and evolutionary path was obtained. Then four parameters with discount rate of water charges, incentive rate, plant income increasing rate, contribution rate of farmers on the choice of cooperation strategies were simulated. It was indicated that effort strategy of project company and participation strategy of farmers were interrelated from perspective of evolutionary game, and effort strategy of project company was improved discount rate of water charges, incentive rate and plant income increasing rate of farmers, and participation enthusiasm of farmers was improved; thus, engineering quality and efficient operation were assured. As a result, the evolutionary path of cooperation strategy between project company and farmers was suggested as effort strategy and participation strategy, respectively, and corresponding measures of company and participation style of farmers were adopted for promoting the formation of the final equilibrium state.