Long term fertilization alters soil microbiological properties and then affects soil organic carbon (SOC) stocks. However, the interrelations of SOC with biological drivers and their relative importance are rarely analyzed quantitatively at aggregate scale. We investigated the contribution of soil microbial biomass, diversity and enzyme activity to C stock in soil aggregate fractions (> 5 mm, 2 − 5 mm, 1 − 2 mm, 0.25 − 1 mm and < 0.25 mm) at topsoil (0–15 cm) from 27-year long term fertilization regime. Compared to CK (no fertilization management), NPS and NPM (inorganic fertilization plus the incorporation of maize straw or composted cow manure) significantly reduced the impact of NP (inorganic fertilizers application alone) on the growth of microbial community, and increased the microbial contribution to C stock. The results showed that microbial variables were significantly correlated with SOC content in > 0.25 mm aggregates rather than in < 0.25 mm aggregates. Fungal variables (fungal, AM biomass, and F/B ratio) and enzyme activities (BXYL and LAP) in > 0.25 mm aggregates explained 21% and 2% on C, respectively. Overall, organic matter (OM) addition could contribute to higher C storage by boosting fungal community and enzyme activity rather than by changing microbial community diversity in macro-aggregates.