Mineral organic complexes are essential for the storage of soil organic carbon (SOC) in agricultural soils. They are also affecting the CO2 emission reduction goals of known as the “doublecarbon target” (carbon peaking and carbon neutrality), as well as a landing point for achieving the 4 per 1,000 carbon enhancement initiative. As a typical soil mineral, calcium (Ca) plays a very critical role in regulating the accumulation of global organic carbon. Although calcium carbonate (CaCO3) has been shown to mediate the SOC accumulation process, especially in northern China, the relationship between Ca and SOC, and the underlying microbial mechanisms remain unclear. In this study, five soils (black soil, light chernozem soil, fluvo-aquic soil, sierozem soil, and loess soil) with different CaCO3 contents (4.29, 17.45, 98.66, 131.85, 143.82 g/kg, respectively) were selected to reveal the relationship among CaCO3, the SOC fraction and the chemical structure, and the bacterial community. The content of CaCO3 was determined by the gas volume method. Solid-state 13C nuclear magnetic resonance (NMR) spectroscopy was used to analyze the chemical structure of SOC, and 16S rRNA gene amplicon sequencing was used to analyze the bacterial community. The results showed that the contents of particulate organic carbon (POC) and mineral-associated organic carbon (MOC) in macro-aggregates were higher than that in micro-aggregates, and that POC was significantly higher than MOC in soil with high CaCO3. With an increase in the CaCO3 content, there was a decrease in the proportion of aromatic C and alkyl C, but an increase in the proportion of O-alkyl C in SOC, the relative abundance of Proteobacteria and Chloroflexi grew, and that of Acidobacteria decreased. Moreover, the overall diversity of the soil bacteria likewise showed a decreasing trend. High CaCO3 soils showed a positive correlation between Acidobacteria and macro-aggregates, and a negative correlation with clay and silt, when compared to low CaCO3 soils. Also, Chloroflexi and Gemmatimonadota showed the opposite relationship with SOC aggregates. CaCO3 influenced the relationship between SOC (fraction and chemical structure) and the bacterial community, resulting in changes in the SOC content within the aggregates. Our results indicate that CaCO3 plays an essential role in the accumulation of SOC and reveal the mechanisms of carbon sequestration in calcareous soils in northern China.