Abstract: Soil organic matter is a complex continuum composed of small molecules from cell lysis and metabolism of plant and microbe. Microbial residues are an important source of soil organic carbon (SOC) and play a vital role in regulating the structure and stability of the SOC pool. Microbial residues and the SOC pool are closely associated with soil microbial activity and are closely linked at the metabolic level. However, direct empirical evidence and in-depth mechanism understanding of how microbial metabolism regulates the contribution of microbial residues to the SOC pool remain scarce. In this paper, we discuss the theoretical basis of the microbial residue contribution to SOC pool from the perspectives of the contribution of microbial residues to SOC pool, the regulation of secondary metabolites on soil carbon turnover and the ecological linkages between microbialresidues and SOC pool. We emphasize that future researches should focus on three areas: 1) investigating the response of the molecular composition and bioavailability of soil secondary metabolites to variations in nutrient input by employing non-targeted exometabolomics, metagenomics, and biomarkers technologies; 2) Elucidating the regulatory effects of soil secondary metabolites on mediating microbial residue contributions to the SOC pool and their context-dependence characteristics; 3) Unraveling the ecological mechanisms by which microbial residues contributing to the SOC pool from the perspective of microbial metabolism. The implementation of the relevant research will no only enrich the ecological theory of soil organic matter formation and stability from a microbial metabolism perspective, but also provide scientific and technological support for climate change mitigation and adaptive strategies in the future.