Microbes are crucial components of soil, and their residue carbon plays a significant role in the formation and stabilization of soil carbon pools. However, current research on microbial residue carbon has predominantly focused on surface soils, with limited studies on deep soils. The patterns of variation along soil profiles and their controlling factors remain unclear. Therefore, this study aimed to investigate the soils from different elevations in the Wuyi Mountains, specifically focusing on the organic layers (0–10 cm) and mineral layers (30–40 cm). Amino sugars were utilized as biomarkers for the microbial residue, and the RDA (redundancy analysis) method was employed to analyze the patterns of microbial residue carbon in different soil layers and to identify the factors that control them. The results indicate that there are significant differences in the microbial residue carbon content and its contribution to soil organic carbon (SOC) between the different soil layers. Specifically, between the organic layer and the mineral layer, the microbial residue carbon content exhibited an increasing trend, whereas its contribution to SOC decreased. This finding suggests that soil layer type has a notable impact on microbial residue carbon content and its contribution to SOC. Moreover, fungal residue carbon content was found to be higher than bacterial residue carbon content in both soil layers. However, the ratio of fungal residue carbon to bacterial residue carbon gradually decreased between the organic layer and the mineral layer. This implies that although fungal residue carbon remains dominant, the contribution of bacterial residue carbon to the soil carbon pool increases as the soil transitions to the mineral layer. The total soil carbon content, elevation, and C/N ratio exhibited positive correlations with fungal and bacterial residue carbon, indicating their significant roles in the accumulation of microbial residue carbon in soils. Notably, elevation emerged as a key regulating factor in the accumulation of microbial residue carbon, explaining 85.8% and 67.9% of the variations observed in the organic layer and the mineral layer respectively. These research findings contribute to a better understanding of the soil carbon cycling process and its mechanisms, providing a scientific basis for developing strategies to enhance soil carbon sequestration by manipulating micro-organisms.