Plantation is an economical and effective method of ecological restoration, which is also a common means to increase soil organic carbon (SOC) content. However, the effects of vegetation types on SOC accumulation and δ13C distribution during ecological restoration are still not clear. Therefore, we evaluated the soils under four types of restoration measures: plantation (PL, dominated by Olea europaea ‘Leccino’), grasslands [GLs, Setaria viridis], croplands [CLs, Zea mays] and shrublands (SLs, Lycium chinense Mill), after 11-year restoration. SOC and the natural stable carbon isotope abundance in four recovery modes were determined, while amino sugars (ASs) and lignin phenols (LPs) were used as biomarkers to identify microbial- and plant-derived carbon, respectively. The results showed that SOC, AS, and LP decreased with the increasing of soil depth, and SOC and LP showed the same trend in topsoil (0–20 cm). ASs in subsoil (40–50 cm) were significantly higher in GLs than that in CLs and the PL, while fungi residue carbon in GLs was significantly higher in subsoil. The δ13C in topsoil was mainly affected by plant factors, especially by litter. With the increasing soil depth, the effect of plants on δ13C decreased, and the effect of microorganisms increased. Vegetation types could affect SOC and δ13C by influencing plant inputs in topsoil. In the subsoil, differences in microbial compositions under different vegetation types could affect δ13C enrichment. The study revealed the effects of vegetation types on SOC accumulation and δ13C distribution during ecological restoration, emphasized that vegetation types can affect SOC accumulation by influencing the plant input of topsoil and the microbial compositions in subsoil, and provided a reference for the development of management policies in restoration areas.