Crop rotation enhances soil fertility and health by modulating microbial communities, with soil organic carbon (SOC) dynamics governed by aggregate–microbial interplay. To date, the effects of different crop rotations on SOC fractions and relevant bacterial communities at aggregate scales remain uncertain. Here, a 17-year field experiment was used to reveal the effects of maize monoculture (MM), soybean monoculture (SS), and maize and soybean rotation on the SOC fractions and bacterial communities. Compared with the SS treatment, only the MS treatment significantly increased the particulate organic carbon (POC) content at the aggregate scale. Nevertheless, higher mineral-associated organic carbon (MaOC) contents were observed under the MS and MM treatments than under the SS treatment. The microbial co-occurrence networks for macro- and microaggregates were divided into three main ecological clusters. The specific taxa in Cluster 1 and Cluster 2 are involved in SOC fraction turnover within macro- and microaggregates, respectively. In total, the Vicinamibacteraceae-driven Cluster 1 community dominated the MaOC turnover process within macroaggregates, whereas the Actinobacteria- and Pyrinomonadaceae-driven Cluster 2 communities changed the MaOC turnover process within microaggregates. This study strengthens our understanding of the role of the microbial community in the accumulation of SOC fractions under different crop rotation practices.