Terrestrial ecosystems are vital carbon sinks that can effectively restrain the rise in CO2 in the atmosphere. How ecosystem carbon storage (CS) in semi-arid watershed areas with slow urbanization is affected by comprehensive factors of the environment and land use, along with its temporal and spatial changes has still not been fully explored. Notably, there is a paucity of research on the temporal and spatial changes and development trends of CS in the rapid deformation belt of slopes from the eastern margin of the Qinghai–Tibet Plateau to the Loess Plateau. Taking Bailong River Basin (BRB) as an example, this study combined GeoSOS-FLUS, the InVEST model, and localized “social–economic–nature” scenario to simulate the long-term dynamic evolution of CS. The aim was to study how topographic factors and land use change, and their interactions impact carbon sinks and gradient effects in steep-slope areas, and then find out the relationship between carbon sinks and topographic factors to explore strategies to improve regional carbon sink capacity. The results showed that the following: (1) CS in BRB increased year by year, with a total increase of 558 tons (3.19%), and showed significant spatial heterogeneity, mainly due to the conversion of woodland and arable land; (2) except for land use type, the relationship between CS and topographic gradient is inverted U-shaped, showing a complex spatial response; and (3) it is estimated that by 2050, under the arable land protection and natural development scenarios, CS will decrease by 0.07% and 0.005%, respectively, encroachment on undeveloped mountain areas, while the ecological protection scenario gives priority to protecting the carbon sinks of woodland and grassland, and CS will increase by 0.37%. This study supports the implementation of targeted ecological protection measures through topographic gradient zoning, provides a reference for policy makers in similar topographic regions to effectively manage the spatial heterogeneity of CS, and helps further strengthen global and regional climate change mitigation efforts.
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