Paddy soil often undergoes frequent dry-wet alternation. The change in water status not only affects the physical and chemical properties of the soil, but also changes the structure and diversity of the soil microbial communities, which in turn determines the rate of soil organic carbon mineralization. However, the effects of different water conditions and soil microbial biomass levels on the process of soil organic carbon mineralization and its mechanisms are still unclear. Therefore, this study took typical subtropical paddy soil as the research object, applied a laboratory incubation experiment with two water treatments of dry-wet and continuous flooding, and reduced the soil microbial biomass through chloroform fumigation, thereby obtaining high and low soil microbial biomass carbon contents, to elucidate the influencing mechanisms of microbial biomass and water conditions on organic carbon mineralization in paddy soil. The results showed that during the first 30 d of incubation, the dry-wet treatment was in a non-flooded stage and its cumulative CO2 emissions were significantly lower than those of the continuous flooded treatment. After 30 d, the dry-wet treatment entered the flooded stage. The difference in the cumulative CO2 emissions of the soils with a high microbial biomass carbon content between the dry-wet and continuous flooding treatments gradually decreased, and there was no significant difference on day 78. In the soil with a low microbial biomass carbon content, the cumulative CO2 emissions of the dry-wet treatment on day 78 was still significantly lower than that of the continuous flooded treatment. The soils with a low microbial biomass carbon content showed a faster CO2 emission rate at the beginning of the incubation period (first 20 d), which was 1.1-6.1 times greater than that of the high microbial biomass carbon soils owing to their high soil dissolved organic carbon (DOC) content, and the CO2 emission rate then gradually decreased until it was below that of the soil with a high microbial biomass carbon content. The soil organic carbon mineralization rate became stable later in the incubation period (days 45-78). The stable mineralization rate of the high microbial biomass carbon soil was 20%-30% higher than that of the low microbial biomass carbon soil. The multiple regression analysis results showed that the decrease in the soil DOC content (ΔDOC) and the increase in the Fe2+ content (ΔFe2+) significantly affected the change in cumulative CO2 emissions (ΔCO2) under continuous flooding conditions, but had no effect on ΔCO2 during the flooding stage of the dry-wet treatment. The correlation analysis showed that the daily CO2 emission rate of soils with high microbial biomass carbon was significantly positively correlated with glucosidase activity under dry-wet treatment and significantly negatively correlated with acetylglucosaminidase (NAG) and peroxidase activities under continuous flooding treatment. In the low microbial biomass carbon soils, the daily CO2 emission rate of the continuous flooding treatment was negatively correlated with the NAG activity, but showed no correlation with enzyme activities under dry-wet management. In summary, the cumulative CO2 emissions of dry-wet treatment were lower than those of continuous flooding treatment, and the difference was significant in soils with low microbial biomass carbon. The size of the soil microbial biomass determined the level of the stable soil organic carbon mineralization rate. The amount of soluble organic carbon and iron reduction affected the soil CO2 emissions under continuous flooding conditions, and the soil water conditions affected the daily CO2 emission rate and its key influencing enzymes. This study provides data and theoretical support for the carbon cycle and carbon sequestration potential in paddy soil.