The River and Lake Chief System has gradually evolved from the exploration of grassroots river and lake governance to the institutional innovation of national governance behavior, and its policy evolution is inseparable from the policy guidance of governments at all levels. The paper built the three-dimensional analysis framework of “policy stage-policy tool-policy objective”, combed and summarized 131 policy texts of the central government, national ministries and commissions and provincial River and Lake Chief System in China since 2008.The results show River and Lake Chief System has gone through three stages: regional practice, comprehensive promotion, and improvement and deepening. The policy objective has shifted from focusing on the spatial supervision of rivers and lakes to comprehensive river and lake management with an emphasis on ecological priorities. The policy tools are gradually shifting from command-and-control to market incentives and voluntary participation, but remain predominantly command-and-control. In the future, the government should promote the transformation of the River and Lake Chief System to have an effective evolution, optimize and improve policy tools to achieve multi-party coordinated participation, and the policy goal should be changed from river governance to watershed governance, and accelerate the transformation of the “River and Lake Chief System” into “River and Lake Permanent Governance”.