Abstract: The mineral composition in coal has a significant impact on the biogenic gas production process, but the response mechanisms between clay minerals and microbial communities as well as heavy metal resistance genes under different coal ranks remain poorly understood. Using medium- and low-rank coals as research subjects, biogenic gas production experiments were conducted under controlled variations in clay mineral content to systematically evaluate the influence of clay minerals on biogenic gas production performance and the distribution characteristics of microbial heavy metal resistance genes. Techniques such as X-ray Diffraction (XRD), Scanning Electron Microscopy–Energy Dispersive Spectroscopy (SEM-EDS), and Inductively Coupled Plasma Mass Spectrometry (ICP-MS) were employed to characterize the mineral phase composition, microstructure, and elemental occurrence characteristics of the coals. Metagenomic sequencing was further used to analyze changes in microbial community structure and the abundance of heavy metal resistance genes, exploring the intrinsic relationship between clay mineral content and biogenic gas production performance. The results indicate that clay mineral content and coal rank jointly constrain the biogenic methane generation process. In low-rank coal, as clay mineral content increased, methane production decreased from 6.30 mL/g to 3.47 mL/g, indicating inhibited biogenic gas production. In contrast, in medium-rank coal, an increase in clay mineral content raised methane production from 3.45 mL/g to 5.28 mL/g, significantly enhancing gas production efficiency. Changes in gas production performance were accompanied by adjustments in mineral phase composition and microstructure, with decreased contents of elements such as Al and Fe and relative enrichment of elements like Cu and Zn. Metagenomic analysis revealed that high gas production systems exhibited higher abundances of heavy metal resistance genes related to copper and arsenic transport (copA, copB, arsB), suggesting that transmembrane transport processes help reduce the bioavailability of heavy metals. Microbial community structure analysis showed that high gas production systems were dominated by the Bacteroidota phylum, whose abundance was significantly positively correlated with heavy metal resistance genes, with groups such as Lactobacillaceae and Bacteroidales identified as potential gene hosts. Correlation network analysis further revealed synergistic distribution patterns among heavy metal resistance genes and between these genes and bacterial groups. The study demonstrates that clay minerals in coal can indirectly regulate biogenic methane generation by influencing microbial community structure and the distribution of heavy metal resistance genes, providing new theoretical insights for research on the formation mechanisms of biogenic gas in coal seams and for coal bioconversion and clean resource utilization.