Abstract: The ecological compensation mechanism in the Yellow River Basin is an effective means to resolve the dilemma of ecological protection and environmental governance in the Yellow River Basin and achieve high-quality development in the Yellow River Basin. The ecological compensation mechanism of the Yellow River Basin in Henan Province has experienced from a slow start stage driven by strong policies, to a rapid development stage driven by policies and endogenous forces, and then to a consolidated and fixed stage of strengthening institutional construction. The ecological compensation mechanism of the Yellow River Basin in Henan Province is faced with some problems, such as the dilemma of collective action, the inappropriate involvement of vertical forces and the lack of participation of diversified forces, which affects its realization effect. Incorporating basin ecological compensation into the "River Chief System" system can give full play to the vertical administrative authority, horizontal cooperation platform and diversified subject advantages of the "River Chief System", and promote the effective operation of the ecological compensation mechanism in the Yellow River basin.