AbstractMicrobial communities regulating multiple ecosystem functions in agricultural ecosystems remain unclear, limiting our ability to predict how agricultural systems will respond to nutrient management. Here, we assessed the effects of 5‐year different fertilization treatments (CK, no‐fertilization; M, organic fertilization; MNPK, combined inorganic and organic fertilization; NPK, inorganic fertilization) on the bacterial and fungal composition, co‐occurrence networks complexity and the relationship of keystone taxa with soil multifunctionality. Our results showed that fertilization shifted the bacterial and fungal community composition. The increased nodes of degree and decreased average path length with the application of organic fertilizer suggested a more stable network. The improved soil multifunctionality was also observed in combined organic and inorganic fertilization treatment, which positively correlated with the fungal community composition rather than bacterial, indicating that fungi are important in driving soil functions. Notably, the keystone taxa fOTU3995 and fOTU2868 belong to Sordariomycetes and were correlated with soil organic carbon, total nitrogen, total phosphorus, and alkaline phosphatase. These indicated that the keystone taxa play an important role in increasing in soil nutrient, C cycling, and P cycling. Together, our findings highlight that combined organic and inorganic fertilization increases the network complexity and soil multifunctionality, further confirming the role of keystone taxa Sordariomycetes in driving soil multifunctionality. This suggested that combined organic and inorganic have the potential to preserve agroecosystem sustainability and strengthen the role of microorganisms in ecosystem functions.