Land-use change affects the regional spatial patterns of carbon storage. Exploring the relationship of land use with carbon storage is crucial for optimizing land-use structure and sustainable development. We explored the spatial and temporal patterns of land use and carbon-storage changes in urban agglomerations in the middle reaches of the Yangtze River for 2035 using the PLUS-InVEST model. Natural, urban, and ecological development scenarios were considered. Land-use changes comprised increases in arable and construction lands and continuous losses in forest land from 2000 to 2020. Carbon storage decreased by 1 × 106 t, with forest conversion to cropland and construction land being the main decreasing drivers. The carbon storage of natural and urban developments decreased by 0.26 × 106t and 0.32 × 106t, while it increased by 0.16 × 106 under ecological development. NDVI (0.588) had the highest explanatory power for the spatial variation of carbon storage, followed by slope (0.454) and elevation (0.391). Natural environmental factors dominate the spatial variation of carbon storage. The combination of multiple factors affected the spatial and temporal variations of carbon storage. The interaction between soil erosion and elevation, NDVI, and annual rainfall was weakened, while the that of other factors was enhanced.