The dynamics of eroded and retained soil organic carbon (SOC) may provide critical clues for evaluating impacts of soil erosion on global carbon cycling. Distribution patterns of soil aggregates in eroded and deposited environments are shaped by selective transport of water erosion. Therefore, detecting the pattern of SOC mineralization in soils dominated by aggregates of different sizes is essential to accurately explore the dynamics of eroded and retained SOCs in eroded and deposited environments. In the present study, the characteristics of SOC mineralization and its relationship to microbial dynamics in subtropical red soils dominated by different sizes of soil aggregates were investigated. The results demonstrated that the SOC mineralization rate of soils dominated by graded aggregates were significantly different, indicating that SOC mineralization in eroded and deposited environments are shaped by selective transport of water erosion. The highest mineralization rate was found in soils containing 1-2 mm aggregates at the initial stage of the experiment, and the daily average mineralization rate of the < 0.5 mm aggregates was significantly higher than that of the 2-3 mm aggregates. During the incubation, fungal communities exhibited a low dynamic character, whereas the composition of bacterial communities in all treatments changed significantly and had obvious differences relative to each other. Bacterial species diversities and relative abundances in the <0.5mm and the 2-3mm aggregates showed opposite dynamic characteristics. However, there were no statistical interactions between the dynamics of microbial communities and the changes of SOC or soil water content. Changes in bacterial community structure had no significant impact on the mineralization of SOC, which might be related to the quality of SOC or the specific utilization of carbon sources by different functional groups of microorganisms. Mineralization of the eroded and retained SOCs with specific qualities in relation to their functional microorganisms should be further explored in the future.