Vegetation restoration is an effective strategy to improve soil organic carbon (SOC) sequestration in the degraded ecosystems. However, the responses of SOC fractions, stabilization, and sequestration capacity to the managed and natural vegetation restoration in the karst region are poorly understood. Here, using cropland as a control, we compared the managed plantation and naturally recovered shrubland after 15 years of vegetation restoration in a typical subtropical karst depression. The SOC, particulate organic carbon (POC), mineral-associated organic carbon (MOC), readily oxidizable carbon (ROC), recalcitrant index (RI), and relative sequestration capacity (SCS_capacity) were measured. We found that the contents of SOC, POC, and ROC in both plantation and shrubland were significantly higher than those in the cropland, whereas MOC showed no significant difference among the three land-use types. We also found that the contents of POC and ROC in the shrubland were significantly higher than those in the plantation. Furthermore, compared with cropland, the RI in the plantation and shrubland were significantly decreased, whereas the relative sequestration capacity of SOC showed no significant differences. Our results indicated that vegetation restoration over a relatively short period (15 years) mainly improved the active SOC fractions. Moreover, the natural vegetation restoration was more beneficial to the active SOC fraction accumulation than the managed vegetation restoration. However, the decreased soil carbon stabilization following vegetation restoration emphasizes the necessity of avoiding human disturbances of the vegetation restoration sites to maintain soil carbon sequestration.