This study aimed to delve deeper into the alterations in the microbial residual carbon (MRC) accumulation in the Yangtze River’s wetland ecosystems as a consequence of afforestation and to evaluate their impact on soil organic carbon (SOC). The hypothesis posited that afforestation could foster soil aggregation by augmenting arbuscular mycorrhizal fungi (AMF) hyphae and glomalin-related soil protein (GRSP) in deep soil, thereby suppressing the proliferation of genes pivotal to microbial residue decomposition and enhancing MRC accumulation. We collected soil samples at 0–20, 20–40, 40–60, 60–80 and 80–100 cm respectively. Metagenomic sequencing, the quantification of soil amino sugars and MRC, soil aggregate distribution profiling and the measurement of AMF mycelium length density alongside GRSP levels were analyzed. Our findings showed that afforestation notably elevated the concentration of soil amino sugars and the levels of total and fungal MRC, with increases ranging from 53%–80% and 82%–135%, respectively, across the five soil depths examined, in stark contrast to the eroded, non-afforested control. The role of MRC in the SOC was observed to escalate with increasing soil depth, with afforestation markedly amplifying this contribution within the 40–60 cm, 60–80 cm and 80–100 cm soil layers. The study concludes that the SOC content in the deeper soil horizons post-afforestation witnessed a significant rise, paralleled by a substantial increase in both total and fungal MRC, which exhibited a robust positive correlation with the SOC levels. This underscores the pivotal role that amino sugar accumulation from microbial residues plays in the retention of SOC in the deeper soil layers of afforested regions, challenging the conventional wisdom that plant residues are recalcitrant to decomposition within forested SOC matrices.