Vegetation restoration is a critical strategy for combatting rocky desertification in the karst region. Soil black carbon (BC) contributes to the soil organic carbon (SOC) pool and plays an important role in carbon storage. However, the impact of vegetation restoration on BC accumulation under consistent geological (karst lithology) and climatic conditions is not well known. The distribution of BC in aggregates and its role in SOC also require clarification. We investigated the impact of vegetation restoration on soil aggregate stability and the micro-distribution of SOC and BC across a successional gradient (secondary forest, shrubland, farmland, and wasteland) in a karst rocky desertification area. Results showed that vegetation restoration significantly enhanced soil structural stability, with secondary forest and shrubland exhibiting the highest mean weight diameter (MWD) and geometric mean diameter (GMD). Compared with farmland and wasteland, the proportions of water-stable macroaggregates (> 0.25 mm) in secondary forest and shrubland areas increased to over 73%. SOC, BC and TCa concentrations were highest in secondary forest topsoil and decreased with increasing soil depth, while the BC/SOC ratio increased with depth, indicating the selective preservation of recalcitrant carbon in deeper soil layers. Macroaggregates are mostly responsible for SOC and BC accumulation in each land-type category. A significant positive correlation exists between aggregate stability, TCa and SOC and BC stocks (p < 0.05), suggesting a "carbon dual-protection" mechanism: woody vegetation promotes soil aggregation via enhanced root-soil interactions and organic inputs, while high soil calcium enhances the stability of large aggregates and mineral protection ability. These findings indicate that robust vegetation cover promotes the physical occlusion of BC within stable macroaggregates, protecting it from degradation and erosion. Therefore, prioritizing restoration efforts to the secondary forest stage can improve the long-term carbon sequestration potential and soil erosion resistance in fragile karst ecosystems.