The river-lake chief system is a major institutional innovation to govern and maintain the health of rivers and lakes. Comprehensively promoting the long-term system of rivers and lakes is a key measure and an important starting point the constructing the health of rivers and lakes. Further improvement of the rural river and lake system will play an important role in improving the rural living environment and enhancing farmers’ well-being. Since the implementation of the river-lake chief system，the water environment quality of rivers and lakes in Sichuan has been significantly improved，but there are still blind areas in the management of rivers and lakes in rural areas. Based on the deep integration of the river-lake chief system and rural water environment management，this paper focuses on summarizing the effectiveness of implementing the river-lake chief system in Sichuan，discusses many problems and deficiencies in the current implementation of the river-lake chief system，and puts forward corresponding countermeasures and suggestions.