The Yangtze River Basin, one of China's principal grain-producing regions, is increasingly threatened by soil erosion and rocky desertification. However, the spatiotemporal sensitivity patterns and the combined impacts of natural and anthropogenic factors remain insufficiently understood. In this study, multi-source environmental data-including rainfall, vegetation cover, soil erosion, and topographic characteristics-were integrated with official sensitivity assessment standards. Spatial and temporal variations were quantitatively analyzed using transfer matrix analysis, the coefficient of variation, and the geographical detector method. The results indicate that: (1) In 2022, soil erosion and rocky desertification sensitivities exhibited a 'high in the west, low in the east' spatial pattern. Soil erosion sensitivity generally declined, with vegetation cover identified as the primary controlling factor, while rocky desertification sensitivity remained high in the middle and lower reaches, where rainfall, intensified by extreme weather events, replaced vegetation as the dominant driver. (2) Interactions between natural and anthropogenic factors, such as rainfall and population pressure, exerted a stronger influence on sensitivity than individual factors alone. River distribution, particularly when interacting with vegetation changes, was determined to be the principal driver of rocky desertification. (3) Priority management zones were delineated, with the upper basin identified for soil erosion control and major river-lake systems (Yalong River, Minjiang River, Dongting Lake, and Poyang Lake) for rocky desertification mitigation. These findings enhance the understanding of ecological vulnerability patterns in the Yangtze River Basin and provide a scientific basis for targeted ecological management and sustainable regional development.