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Soil organic carbon (C) and aggregates are the important components of soil fertility and the foundation of sustainable agriculture. The storage and protection of SOC in aggregates is widely regarded as the material basis of soil organic C accumulation. However, current understanding of soil aggregate and its associated organic C is insufficient to elucidate the regulation mechanism of soil organic C. A nine-year field experiment including chemical fertilizer (FR) and organic manure (OM) treatments was set up in the eastern plain of Funiu Mountain, central China. Using chemical analysis, physical sieving as well as nuclear magnetic resonance (NMR) methods, we mainly probed into the response of soil organic C concentration and composition, and C functional groups, water-stable aggregates to different treatments. Furthermore, scanning electronic microscopy (SEM) and partial least square structural equation modelling (PLS-SEM) was conducted to characterise the different size aggregates and to analyse the mechanism of soil organic C accumulation and stabilisation at aggregate scales. After nine years of farming, OM treatment substantially increased soil organic C content (by 3.77 g kg−1) and significantly enhanced the formation of macro-aggregates (> 250 μm), while FR had no significant influence on soil organic C. At the aggregate scale, the amounts of soil organic C, C physical fractions (particulate and mineral-associated organic C), total nitrogen and microbial biomass carbon associated in macro-aggregates (> 250 μm) were obviously higher than that in micro-aggregates and silt + clay fraction, and OM treatment greatly increased the accumulation of soil organic C and its components in macro-aggregates. Moreover, microbial biomass carbon (MBC) amounts in aggregates were remarkably increased (27–116%) by the application of OM. And MBC had a positively effect on the physical fractions of SOC but not on the C chemical structure within aggregates. The present study indicated that soil organic C accumulation mainly rely on macro-aggregates (> 250 μm). Intra–particulate organic carbon (POC) and mineral-associated organic carbon (MOC) within macro-aggregates played an important role in soil organic C accumulation. Meanwhile, soil microbes were a driving force for the accumulation of soil organic C physical fractions (POC and MOC). We concluded that OM treatment accelerated the synergistic process between organic C sequestration and soil aggregation, and showed great potential to increase soil organic C accumulation. [ABSTRACT FROM AUTHOR]