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Liming materials have been extensively used to immobilize heavy metals. Bacteria, archaea, and fungi are sensitive to heavy metals and play critical roles in soil biogeochemical cycling and crop health. However, the responses of bacteria, archaea, and fungi to liming materials in agricultural soils contaminated with heavy metals are still unclear. A field experiment was conducted to assess the effect of liming on the three microbial domains and the potential influencing factors in maize-planted agricultural soil contaminated with Cd and Pb. Using a high-throughput sequencing method, we found that liming materials enhanced copiotrophic bacteria (Proteobacteria, Gemmatimonadetes, and Bacteroidetes), Bathyarchaeota, and arbuscular fungi (Glomeromycota) but suppressed some oligotrophic bacteria (Chloroflexi) and saprotrophic fungi. Notably, soil-available Cd markedly influenced the community composition of prokaryotes but not that of eukaryotes. Similar edaphic factors were correlated with the relative abundance of dominant bacterial and archaeal taxa but with opposite effects. Furthermore, co-occurrence network analysis revealed that the complexity decreased but the fungal nodes and edges increased after liming, indicating that the microbial community was not highly resilient to environmental stresses and the importance of fungi in community structure was enhanced. Overall, these findings suggest that changes in microorganisms resulting from liming facilitate soil biogeochemical cycles but suppress microbial stability, potentially affecting the sustainable use of agricultural soils contaminated with heavy metals. • Liming material was applied to an agricultural soil with Cd and Pb contamination. • Liming enhanced copiotrophic but suppressed oligotrophic microbes. • Liming affected microbial communities by different mechanisms. • Microbial network complexity decreased but the importance of fungi increased. [ABSTRACT FROM AUTHOR]