Land-use change is the main driver of carbon storage change in terrestrial ecosystems. Currently, domestic and international studies mainly focus on the impact of carbon storage changes on climate, while studies on the impact of land-use changes on carbon storage in complex terrestrial ecosystems are few. The Jialing River Basin (JRB), with a total area of ~ 160,000 km2, diverse topography, and elevation differences exceeding 5 km, is an ideal case for understanding the complex interactions between land-use change and carbon storage dynamics. Taking the JRB as our study area, we analyzed land-use changes from 2000 to 2020. Subsequently, we simulated land-use patterns for business-as-usual (BAU), cropland protection (CP), and ecological priority (EP) scenarios in 2035 using the PLUS model. Additionally, we assessed carbon storage using the InVEST model. This approach helps us to accurately understand the carbon change processes in regional complex terrestrial ecosystems and to formulate scientifically informed land-use policies. The results revealed the following: (1) Cropland was the most dominant land-use type (LUT) in the region, and it was the only LUT experiencing net reduction, with 92.22% of newly designated construction land originating from cropland. (2) In the JRB, total carbon storage steadily decreased after 2005, with significant spatial heterogeneity. This pattern was marked by higher carbon storage levels in the north and lower levels in the south, with a distinct demarcation line. The conversion of cropland to construction land is the main factor driving the reduction in carbon storage. (3) Compared with the BAU and EP scenarios, the CP scenario demonstrated a smaller reduction in cropland area, a smaller addition to construction land area, and a lower depletion in the JRB total carbon storage from 2020 to 2035. This study demonstrates the effectiveness of the PLUS and InVEST models in analyzing complex ecosystems and offers data support for quantitatively assessing regional ecosystem services. Strict adherence to the cropland replenishment task mandated by the Chinese government is crucial to increase cropland areas in the JRB and consequently enhance the carbon sequestration capacity of its ecosystem. Such efforts are vital for ensuring the food and ecological security of the JRB, particularly in the pursuit of the “dual-carbon” objective.