The microbial transformation of iodine-bearing organic matter (OM) and iron (Fe) minerals is a critical process that controls the release of iodine (I) to groundwater. However, the roles of functional microbial types, OM molecular characteristics, and microbe-OM interactions in iodine mobilization remain unclear. In this study, groundwater samples with different iodine concentrations were collected from the central Yangtze River basins, China. Using 16S rRNA gene sequencing, we identified sulfur disproportionation and methanogenesis as dominant metabolic processes in relatively low-I (<
300 μg/L) and high-I (>
300 μg/L) groundwater, respectively. Sediment incubation experiments showed that combined sulfur disproportionation and methanogenesis can promote iodine release by 87.1%. Ultrahigh-resolution molecular characterization of the organic components revealed that sulfur-disproportionating microbes may selectively metabolize bioactive OM (e.g., aliphatic compounds and oxygen-poor highly unsaturated compounds), leaving recalcitrant OM (e.g., N-containing oxygen-rich highly unsaturated compounds, polyphenols, and polycyclic aromatic compounds) in groundwater, and methanogenic microbes preferentially consume bioactive OM in low-I groundwater and recalcitrant OM in high-I groundwater. Thus, a cooperative-competitive pattern between methanogens and sulfur disproportionating microorganisms may influence OM degradation and potentially contribute to iodine mobilization. This study highlights that the OM transformation process, driven by biological sulfur disproportionation and methanogenesis, promotes iodine enrichment in alluvial-lacustrine groundwater and improves our understanding of the genesis of geogenic high-iodine groundwater systems.