The reclamation and utilization of natural wetlands can affect the community structure of soil microorganisms. However, knowledge regarding succession of microbial communities during long‐term reclamation and the links with related nutrient cycles is still limited. Using Illumina sequencing, we identified the patterns and environmental drivers of soil bacterial and fungal succession along a 150‐year chronosequence of paddy fields. Soil enzyme activities were determined to characterize functions related to C, N, and P cycles. The results showed that reclamation activity and its history have greatly altered the bacterial community structure and the bacterial groups. This change being mainly reflected in the bacterial genera Halomonas, genera Isosphaera, and family Planctomycetaceae. The change of fungal community was mainly apparent between natural wetlands and paddy fields, manifested as an increase in the classes Sordariomycetes and Dothideomycetes and a significant decrease inthe class Agaricomycetes in paddy fields compared with natural wetland. Compared with fungi, bacteria were more strongly affected by soil chemical nutrient properties and physical properties. Furthermore, the structural equation model indicated that both bacterial and fungal community structure and diversity had a great influence on the C, N, and P cycles. In summary, the bacterial community was more sensitive throughout the history of rice cultivation after reclamation than the fungal community, but both bacteria and fungi may play major roles in soil ecological functions. These findings contribute to the understanding of ecosystem functional mechanisms, which provides a new perspective for the management of natural wetlands.