Microbial residue carbon (MRC) is an important source of soil organic carbon (SOC) formation and plays a vital role in the accumulation and retention of SOC. Vegetation restoration is an effective strategy to restore degraded lands. However, there are no studies on how MRC in the profile changes with vegetation restoration. We evaluated MRC (using amino sugars) accumulation and its contribution to SOC in different soil depths (0-20, 20-50, and 50-100 cm) during vegetation restoration in a severely eroded forest (CK), a restored forest (as ecological restoration management), an orchard (as development management model), and a secondary forest (as ideal control). Microbial biomarkers were extracted from soil profiles and used to measure microbial diversity and microbial community composition (using 16S rRNA). Vegetation restoration, soil depth, and their interaction with each other significantly affected MRC, fungal residue carbon (FRC), and bacterial residue carbon (BRC) contents. The MRC content showed an increasing trend for the four vegetation restoration models in the following order: CK < orchard < restored forest < secondary forest. Furthermore, the contribution of MRC to SOC increased with the increasing soil depth for the restored forest. The rapid accumulation of MRC was substantially influenced by SOC, total nitrogen content, soil pH, bacterial and fungal diversity, bacterial phylum, and fungal phylum. In conclusion, the model of vegetation restoration and soil depth play important roles in the accumulation of soil microbial residue carbon in a red soil erosion area. These findings are pivotal for improving our mechanistic understanding of microbial regulation of SOC preservation during vegetation restoration of a degraded ecosystem.