Land use change directly affects the dynamic balance of regional carbon stocks by altering vegetation cover, soil organic matter, and ecosystem structure. This study uses the Random Forest Classification, SD-FLUS model, and InVEST model to analyze the spatial and temporal evolution of land use and carbon stocks in southwest China from 2000 to 2100 and to reveal the trade-off effect between economic development and ecological protection through multi-scenario simulation (SSP126, SSP245, SSP370, and SSP585). The results show that: (1) From 2000 to 2020, the land use pattern in southwest China is dominated by forest-cultivation-grass. The cumulative area of converted cultivated land reaches 29.51×103km2, which directly causes the loss of carbon stocks of 297.08 Tg. (2) The transformation of cultivated/forest land to construction land causes the construction land area to increase by 121.67%, resulting in a net loss of carbon stocks of 156.38 Tg. Although there is a carbon sink gain of 136.07 Tg from forest growth, it is difficult to offset the carbon loss from the expansion of construction land. (3) In the future, urbanization and ecological policies jointly drive the transformation of land patterns. The area of the carbon sink will expand by 174.56% under the SSP126, indicating that the carbon sink gains through a strict low-carbon pathway. (4) In the high emissions scenario, the uncontrolled expansion of construction land leads to more than 75% of cultivated land conversions. Coupled with the point erosion of forest land and the price scissors phenomenon of shrinking high-value areas and expanding low-value areas, 93.84% of counties fall into a carbon deficit, and ecological resilience faces a serious challenge.