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 an important role in regulating the structure and stability of SOC pool. Microbial residue and organic carbon pool are closely related to soil microbial activity and are closely linked at the metabolic level. However, there is a lack of direct empirical evidence and in-depth mechanism understanding of how microbial metabolism regulates the contribution of microbial residues to SOC pool. In this paper, we discuss the theoretical basis of the microbial residue contribution to soil organic carbon pool from the perspectives of the contribution of microbial residues to soil organic carbon pool, the regulation of secondary metabolites on soil carbon turnover and the ecological linkages between microbial residues and soil organic carbon pool. The author highlighted that future researches should focus on (1) the response of molecular composition and availability of soil secondary metabolites to nutrient input changes by using non-targeted exometabolomics, metagenomics, and biomarkers technologies, and (2) the regulatory effect and its context-dependence of soil secondary metabolites in mediating microbial residue contribution to organic carbon pool, and (3) the ecological mechanism of microbial residues contributing to SOC pool from the perspective of microbial metabolism. The implementation of the relevant research will enrich the ecological theory of soil organic matter formation and stability from the perspective of microbial metabolism, but also provide scientific and technological support for climate change mitigation and adaptive management in the future.