Abstract: To enhance the pertinence and scientificity of small watershed management, by comparing and analyzing the differences and linkages between the two in terms of evaluation objectives, time periods, indicators, and results, lake health assessment and clean small watershed management′s mutual supporting mechanism was explored, and the river and lake health assessment results were used to guide the design of small watershed management measures. The results showed that river and lake health assessment could provide a quantitative basis for the preliminary screening of areas, mid-term measure design, and post-treatment effect evaluation of ecological clean small watersheds, achieving the goal of clear water flows down the mountain, clean water flows into rivers and reservoirs. Integrating river and lake health assessment into the entire process of ecological clean small watershed management can effectively improve the systematicness of soil and water conservation work and the health level of river and lake ecosystems, providing references for river and lake health management based on small watershed units.