Abstract: The ecological protection and high-quality development of the Yellow River Basin is a major national strategy. A thorough analysis of long-term evolution patterns and driving mechanisms of the ecosystem in this region is of great significance for promoting sustainable basin governance. This study aims to systematically reveal the evolutionary characteristics of ecosystem in the Yellow River Basin across different historical times and to identify the dominant driving factors, while proposing evidence-based strategies for ecological protection and restoration. By integrating long-term monitoring data from the National Terrestrial Ecosystem Research Station Network, multi-source remote sensing products, statistical records, and historical documents, this research employs a combination of historical retrospection, spatial analysis, and model simulation to explore the evolutionary processes and driving mechanisms of the ecosystem in the ancient, modern, and contemporary times. The results indicated that: (1) the evolution of the Yellow River Basin ecosystem can be divided into three stages: a relatively stable and slowly degrading stage in ancient times, when natural drivers dominated and human impacts were limited, with broad coverage of forests, grasslands, and wetlands; a stage of rapid degradation in modern times, when population growth and agricultural reclamation led to severe vegetation destruction, desertification expansion, and significant decline in ecosystem services; and a stage of ecological restoration and partial improvement in contemporary times, when the implementation of ecological projects promoted gradual vegetation recovery, with forest, grassland, and wetland areas showing a “U”-shaped change, desertification experiencing an “n”-shaped evolution, and improvements also evident in farmland quality and urban ecological functions. (2) Overall, the ecosystem of the Yellow River Basin has experienced an evolutionary process from natural stability, human-induced degradation to gradual restoration, reflecting the dual characteristics of continuous natural base degradation and intensifying human disturbance. This also marked a shift from disorder and imbalance caused by human activities toward an orderly balance between humans and nature, highlighting the positive outcomes of recent ecological restoration efforts. (3) In ancient times, ecosystem evolution was mainly influenced by climate change, earthquakes, population growth, and wars, with climate being the dominant natural factor and population expansion and reclamation being the main human causes of vegetation degradation. In modern times, extreme climate events combined with wars exacerbated ecological damage. In contemporary times, both climate change and human activities drive ecological changes. Human activities include forestry ecological projects, water and soil conservation measures, industrial and agricultural water use, and urbanization, whose impacts vary significantly across regions and times. In conclusion, future efforts should strengthen research on the coupling mechanisms between climate change and human activities, optimize ecological restoration pathways, and provide scientific support for realizing harmonious coexistence between humans and nature in the basin.