Root exudates can greatly modify microbial activity and soil organic matter (SOM) mineralization. However, the mechanism of root exudation and its stoichiometric ratio of C/N controlling upon paddy soil C mineralization are poorly understand. In this study, we used a mixture of glucose, oxalic acid, and alanine as root exudate mimics, employing three C/N stoichiometric ratios (CN6, CN10, and CN80) to explore the underlying mechanisms involved in C mineralization. The input of root exudates enhanced CO2 emission by 1.8–2.3-fold than that of the control. Artificial root exudates with low C/N ratios (CN6 and CN10) increased the metabolic quotient (qCO2) by 12% over those obtained at higher stoichiometric ratios (CN80 and C-only), suggesting a relatively high energy demand for microorganisms to acquire organic N from SOM by increasing N-hydrolase production. The stoichiometric ratios of enzymes (β-1,4-glucosidase to β-1,4-N-acetyl glucosaminidase) promoting organic C degradation compared to those involved in organic N degradation showed a significant positive correlation with qCO2; the stoichiometric ratios of microbial biomass (MBC/MBN) were positively correlated with carbon use efficiency. This suggests that root exudates with higher C/N ratios entail an undersupply of N for microorganisms, triggering the release of N-degrading extracellular enzymes. This in turn decreases SOM mineralization, implying the C/N ratio of root exudates to be a controlling factor. Our findings show that the C/N stoichiometry of root exudates controls C mineralization by the specific response of the microbial biomass through the release of C- and N-releasing extracellular enzymes to adjust for the microbial C/N ratio.