The illicit connections between sewage and stormwater pipes result in the discharge of untreated sewage into receiving rivers, posing significant odor and health hazards. While thioethers are recognized as key odorants in sewage systems, their distribution in stormwater systems remain poorly characterized. This study analyzed 12 types of thioethers in stormwater pipes sampled at 21 sites in China. Advanced analytical techniques, including Mantel analysis and Structural Equation Modeling, were employed to examine the relationships between overlying water properties, sediment microbial characteristics, and thioether concentrations. Results showed that sediment thioether loads (36.77 ± 50.14 μg S/m; range: 7.24–99.96 μg S/m) were substantially higher than those in the overlying water (12.02 ± 42.52 μg S/m; range: 0.03–92.76 μg S/m), highlighting sediment as a critical pollution reservoir. Dissolved oxygen, NH₃-N, and terrestrial-derived dissolved organic nitrogen were identified as key factors shaping sediment microbiome composition, particularly fermentative, sulfate-reducing, and denitrifying bacteria, which in turn drives thioether formation. Specifically, dominant compounds like dimethyl disulfide and dimethyl trisulfide were found to be produced through the anaerobic fermentation of methionine and redox conversion of methanethiol, as well as the anaerobic fermentation of cysteine and methylation of polysulfides. Humic substances could facilitate methanethiol redox conversion and polysulfide methylation by serving as methyl donors and enhancing electron transfer efficiency. Additionally, NH₃-N may promote microbial metabolism by providing amino groups essential for the synthesis of metabolic precursors. Therefore, effective mitigation of odorous thioethers in stormwater systems necessitates integrated strategies targeting both sulfur-containing organic precursors and nitrogen-rich pollutants.