By providing a scientific foundation for managing regional ecosystem carbon (C) pools, research on the spatial distribution characteristics of regional C stocks can assist in the development of policies on C emissions reduction and sequestration enhancement. Using the GeoSOS-FLUS and InVEST models and explorations of the Bailong River Basin in the past 20 years, the influence of three future scenarios of land use change—natural development (ND), ecological protection (EP) and arable land protection (ALP)—on C storage was modelled. Between 2000 and 2020, there was a gradual increase in C storage in the BRB with a total increase of 5.58 Tg (3.19%), showing notable spatial heterogeneity. The increase in C storage was attributed to land use conversion among woodland, arable land and grassland, with the conversion between woodland and arable land being the primary factor contributing to the increase in C storage. By 2050, C storage under the EP, ALP and NP scenarios was 183.915, 183.108 and 183.228 Tg, respectively. In 2050, C storage under the EP scenario increased by 0.37% compared with that in 2020, and decreased by 0.07% and 0.005% under the ALP and NP scenarios, respectively. In contrast to the other scenarios, the EP scenario prioritised the protection of the woodland and grassland C sinks, which has significant implications for future planning.