The impact of vegetation restoration on soil structure, nutrients, and microorganisms in eroded areas has been extensively studied, but the effect of vegetation restoration on carbon-sequestering bacterial communities and their associated carbon fixation capacity remains largely unknown. In this study, we focused on the 0–20 cm soil layer in eroded and vegetation restoration sites in areas of southern China that have been severely affected by soil erosion and utilized 13C stable isotope labeling and high-throughput sequencing technologies to investigate the influence of vegetation restoration on carbon-sequestering bacterial communities and their carbon sequestration potential. Compared with eroded areas, vegetation restoration areas presented greater soil nutrient contents and greater diversity of bacteria with carbon sequestration functions. Vegetation restoration also altered the composition of carbon-sequestering bacterial communities by increasing the soil alkali-hydrolyzable nitrogen content, with the dominant carbon-sequestering bacteria shifting from Nocardia to Bradyrhizobium. However, the microbial carbon sequestration rate in soil erosion areas significantly increased by 2.15 times compared with that in vegetation restoration areas. Among the factors considered, pH (68.90 %, P = 0.000) was identified as the primary explanatory factor regulating changes in the microbial carbon sequestration rate. Our results are important for revealing the role of vegetation restoration in the global carbon cycle and elucidating the role of microorganisms in the soil carbon cycle.