Karst regions, characterized by thin soil layers, severe rocky desertification, and fragile vegetation, hold significant scientific value for achieving China's "dual-carbon" goals. This study focuses on Zhijin County in Guizhou Province, integrating provincial carbon density data with forest resource inventory data. By constructing a model to adjust aboveground forest carbon density (AGC) estimation parameters and utilizing the InVEST model alongside hotspot analysis, the research systematically examines the spatiotemporal heterogeneity of carbon storage from 2000 to 2020. These findings provide actionable strategies for enhancing carbon sequestration efficiency in ecologically fragile regions, supporting China's "dual-carbon" policy goals. Key findings include: (1) Carbon storage exhibits a "growth-turning point" two-phase pattern, increasing by 0.46% from 2000 to 2015 but decreasing by 3.31% in 2020 due to construction land expansion. (2) There are significant differences in carbon storage among ecological engineering projects, with the highest carbon storage found in the "Grain-for-Green Program" project area and the lowest in the "National Rocky Desertification Control Program" area. (3) Elevation is the primary controlling factor for carbon storage, with rocky desertification showing notable spatial differentiation. This study provides theoretical support for the precise regulation of ecological programs and the development of high-precision carbon storage models in karst regions.