Abstract: Exploring the long-term evolutionary processes and driving mechanisms of the Yellow River Basin’s ecosystems is a prerequisite for gaining a profound understanding of the evolution of regional ecological security landscape. This study integrated long-term monitoring data from the National Forestry and Grassland Administration’s Terrestrial Ecosystem Research Network, multi-source remote sensing products, statistical data, and historical literature. Employing a method that combines historical retrospection with spatial analysis, it systematically analyzed the evolutionary characteristics of the basin across three historical periods, i.e. ancient, modern and contemporary, identified the dominant driving factors, and proposed targeted conservation and restoration strategies. The results indicated: (1) the evolution process can generally 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 “inverted U”-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, degradation due to human disturbance to gradual restoration, reflecting the interactive nature of natural systems and human interference. This trajectory represents a gradual shift from the disorderly imbalance caused by human disturbance toward an ordered equilibrium of harmony between humans and nature, and also demonstrates 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. (4) Guided by the principle of “zonal strategies, categorized management, and systemic coordination,” targeted governance strategies have been proposed for five key areas: zonal ecological management, soil and water conservation and desertification control, wetland restoration, farmland optimization, and urban ecology. 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.