The ecological protection and high-quality development of Yellow River Basin are related to the future plan of the great rejuvenation of the Chinese nation. County-level ecological governance is directly related to the overall situation of ecological civilization construction, as well as the realization of the long-term goals during the 14th Five-Year Plan period and even 2035. Therefore, county-level ecological governance is of great significance to achieve ecological protection and high-quality development in Yellow River Basin. This paper expounds the era value of county-level ecological governance of Yellow River Basin, analyzes the key problems faced by county-level ecological governance of Yellow River Basin from four aspects: environmental status, cognitive level, supporting capacity and guarantee system, and proposes five key areas of county-level ecological governance of Yellow River Basin, namely, the protection of the ecological environment, the control of environmental pollution, the restoration of the ecological environment, the construction of the ecological environment and agricultural green development. This paper systematically puts forward countermeasures and suggestions to achieve county-level ecological governance of Yellow River Basin from the aspects of strengthening top-level design, promoting scientific and technological innovation, increasing capital investment, focusing on talent cultivation, establishing a long-term mechanism, and improving policy system.