The Yellow River Basin is an important ecological barrier in China. Due to its sensitive and fragile ecological nature, severe problems have arisen in some regions. Therefore, there is a need to conduct systematic planning for the ecological management of this basin to address prominent problems. To further promote the ecological protection and high-quality development of the Yellow River Basin, this study analyzes the major challenges regarding ecological protection in the region and summarizes the major problems in terms of the investment in ecological management, construction of ecological monitoring networks, and modernization of ecological management capacities. To this end, we propose a strategic system framework for integrated ecological governance in the Yellow River Basin led by major projects. Integrated ecological governance should consider the spatial differentiation of the upper, middle, and lower reaches and adhere to the principles of systematic design. Moreover, measures need to be taken to adapt to local conditions, and land and water should be linked for joint prevention and control. Additionally, major projects are required to lead integrated governance, including mountainriver-forest-farmland-lake-grass-sand integrated protection, comprehensive environmental pollution control, and ecological management modernization projects. Considering the urgency and necessity of solving current ecological problems, we propose the following suggestions: (1) establishing an ecological management project library, (2) implementing major projects in stages and in batches, (3) conducting entire-process supervision and effectiveness evaluation of major projects, and (4) strengthening scientific and technological support for major projects.