Studying the temporal and spatial variation characteristics and driving factors of carbon reserves in the middle reaches of the Yangtze River urban agglomeration is crucial for achieving sustainable development and regional ecological conservation against the backdrop of the “double carbon” plan. Based on three periods of land use data from 2000 to 2020, combined with the InVEST model(Version 3.14.2), the spatiotemporal changes in carbon storage in the urban agglomeration in the middle reaches of the Yangtze River were analyzed. The PLUS model (Version 1.3.5) was used to predict three scenarios of natural development, urban development, and eco-development in the urban agglomeration in the middle reaches of the Yangtze River in 2035 and estimate the carbon storage of the ecosystems under different scenarios, and it used optimal parameter GeoDetectors (Version 4.4.2) to reveal the driving factors affecting the spatiotemporal differentiation of carbon storage. The results show that farmland and construction land area increased and forestland area continued to decrease from 2000 to 2020. Carbon storage decreased by 1 × 106 t, with forestland conversion to farmland and construction land being the main decreasing drivers. The carbon storage of natural and urban developments decreased by 0.26 × 106 t and 0.32 × 106 t, while it increased by 0.16 × 106 under ecological development. The results of the factor detector showed that the NDVI (Normalized Difference Vegetation Index) had the highest explanatory power on the spatiotemporal variation in carbon storage (q = 0.588), followed by the slope (q = 0.454) and elevation (q = 0.391), and the explanatory power of natural environmental factors on the spatiotemporal variation in of carbon storage was dominant. The interaction detector results showed that the spatiotemporal variation in carbon storage was affected by multiple factors, the interaction intensity between each driving factor was stronger than that of a single factor, and the synergy between the NDVI and slope was the strongest, at q = 0.646.