Ecological protection and high-quality development in the Yellow River Basin has become a major national strategy. The protection and management of the Yellow River has always been an important event for social stability and people’s happiness. The Yellow River is the most complicated and refractory river in the world. After years of ecological treatment and restoration，the water quality of the downstream river has been improved obviously. However，the practical results of water pollution treatment are still not optimistic. There are many contradictions in ecological restoration，and there is a lack of ecological judicial mechanism and cross-regional and cross-sectoral linkage mechanism in the basin. It is necessary to comprehensively drop the internship of General Secretary Xi Jinping’s Ecological Civilization Thought，start with the reform of the judicial system，give full play to the functions of political，legal and administrative law enforcement departments，improve the specialized trial supervision institutions，improve the centralized jurisdiction of cases，and improve the cross-regional and inter-departmental management coordination and judicial cooperation linkage mechanism of environmental protection. Social participation，information sharing，promote diversified solutions to wading disputes，promote the legislation of the Yellow River Protection Law in a timely manner，and fundamentally solve the problems of environmental ecological protection and pollution control in the Yellow River Basin across administrative regions.