At present, the problem of rural river pollution in China is very severe. Clarifying the relationship among the stakeholders is the key to solve the dilemma of rural river management under the River Chief System. Under the assumption of the stakeholders' bounded rationality, the evolutionary game tool is used to study the problem of rural river management under the River Chief System. Firstly, three important stakeholders are defined in the rural river management: rural river chiefs, functional institutions and rural residents, and their strategic choices as well as interrelationships are analyzed. Secondly, the evolution of the three stakeholders is discussed by using the evolutionary game tool, and the gradual stability of the evolution model is analyzed. The evolutionary stability strategies of different stakeholders are discussed. Finally, according to the model analysis results and the influences of non-set conditions, some suggestions for the rural river governance issues are proposed for the smooth implementation of the river system in rural areas, such as standardizing the performance evaluation criteria for river chiefs, improving the reward and punishment mechanism of functional institutions, and constructing the information platform of River Chief System.