Background and aims <p>Acid Mine Drainage (AMD) is an environmental pollutant, and the infiltration of such substances into agricultural soils, such as rice paddies, alters soil physicochemical properties and poses a serious threat to soil microorganisms. However, the specific effects of AMD on microbial diversity, community structure and species interactions in rice soils are still unclear.</p> Method <p>We conducted a simulation experiment with rice grown on AMD-irrigated contaminated soil and clear-water-irrigated contaminated soil as test groups and rice grown on clear-water-irrigated uncontaminated soil as control group. Soil samples (non-rhizosphere) were obtained from rice cultivation pots at the seeding, tillering, heading, and maturing stages. Amplicon sequencing of the 16S rRNA gene hypervariable regions (V3–V4) was performed to examine the relationships between bacterial and archaeal community structures and soil physicochemical properties.</p> Results <p>Dominant bacterial genera in AMD-irrigated soils included <i>Candidatus Solibacter</i>, <i>Thiobacillus</i>, and <i>Candidatus Koribacter</i>, which are adapted to acidic and metal-rich environments. In contrast, control soils were dominated by <i>Anaeromyxobacter</i>, <i>Haliangium</i>, and <i>Sphingomonas</i>. Archaeal diversity was higher in contaminated soils, with <i>Methanosarcina</i> and <i>Methanospirillum</i> showing increased relative abundance, particularly under clean water irrigation. Co-occurrence network analysis revealed that microbial communities in control soils had more complex and stable interactions than in contaminated soils, with key bacterial genera such as <i>Candidatus Solibacter</i> and <i>Desulfovibrio</i> acting as crucial connectors. Archaeal networks in contaminated soils were less connected, indicating lower network efficiency under stress.</p> Conclusions <p>In conclusion, AMD contamination in rice soils markedly diminishes microbial diversity and restructures community interactions and ecological dynamics.</p>