Black-odorous urban rivers can serve as reservoirs for heavy metals and other pollutants, in which sewage-derived labile organic matter triggering the water blackening and odorization largely determine the fate and ecological impact of the heavy metals. Nonetheless, information on the pollution and ecological risk of heavy metals and their reciprocal impact on microbiome in organic matter-polluted urban rivers remain unknown. In this study, sediment samples were collected and analyzed from 173 typical black-odorous urban rivers in 74 cities across China, providing a comprehensive nationwide assessment of heavy metal contamination. The results revealed substantial contamination levels of 6 heavy metals (i.e., Cu, Zn, Pb, Cr, Cd, and Li), with average concentrations ranging from 1.85 to 6.90 times higher than their respective background values in soil. Notably, the southern, eastern, and central regions of China exhibited particularly elevated contamination levels. In comparison to oligotrophic and eutrophic waters, the black-odorous urban rivers triggered by organic matter exhibited significantly higher proportions of the unstable form of these heavy metals, indicating elevated ecological risks. Further analyses suggested the critical roles of organic matter in shaping the form and bioavailability of heavy metals through fueling microbial processes. In addition, most heavy metals had significantly higher but varied impact on the prokaryotic populations relative to eukaryotes.