Much research has been devoted to investigating how water-extractable organic carbon (DOC) concentration and microbial activity regulate soil organic carbon (SOC) mineralization when soils are saturated with water. However, the relationships of DOC chemical structure and microbial community composition with SOC mineralization, as well as the relative contributions of microbial decomposers and their substrates on the mineralization rate have rarely been examined. In a laboratory experiment, we incubated two typical cropland soils (an Entisol and a Mollisol) of China for 360 days under submerged and non-submerged conditions, and we evaluated the concentration and chemical structure of soil DOC, soil microbial metabolic potential and community composition by using total C/N analysis, solution-state H NMR, Biolog EcoPlates, and 16S rRNA amplicon sequencing, respectively. The results showed that submergence significantly increased DOC concentration (P < 0.01) and microbial activity (P < 0.001) and changed DOC chemical structure in the Entisol (P < 0.01). In the Mollisol, it significantly increased the rate (P < 0.01) and cumulative extent (P < 0.001) of SOC mineralization and DOC concentration (P < 0.01) as well as altering the composition of the microbial community (P < 0.001). Moreover, the SOC mineralization rate was better explained by microbial community composition (Entisol: SPC = -0.71, P < 0.001; Mollisol: SPC = 0.92, P < 0.001) than by DOC concentration (Entisol: SPC = 0.21, P > 0.05; Mollisol: SPC = 0.30, P < 0.05) or DOC chemical structure (Entisol: SPC = 0.12, P > 0.05; Mollisol: SPC = -0.45, P < 0.001). Our study revealed that the bacterial community composition had a close relationship to the rate of submergence-induced SOC mineralization in both soils, but only DOC concentration and chemical structure were effective predictors of mineralization rate in the low-pH Mollisol.