The　complex　relationships　between　the　molecular　composition　of　dissolved　organic　matter　(DOM)　and　microbial　communities　are　essential　for　maintaining　the　stability　of　aquatic　ecosystems.　This　study　comprehensively　analyzed　the　characteristics　and　potential　effects　of　DOM　molecular　composition　as　well　as　the　relationship　between　microbial　communities　and　DOM　molecular　composition　in　sediments　from　the　Beiyun　River,　Beijing,　China.　The　results　showed　that　the　content　of　DOM　in　Beiyun　River　sediments　was　9.93-41.57　g/kg,　mainly　composed　of　lignin-like　(36.75%)　and　protein-like　(17.79%)　substances.　Compared　with　other　rivers　affected　by　anthropogenic　activities,　the　higher　content　of　labile　substances　in　the　Beiyun　River　increased　the　risk　of　nutrient　release.　At　the　same　time,　1402　molecules　remained　stable　in　each　sample,　most　of　which　were　refractory　lignin-like　substances　and　protein-like　substances　carrying　ester　groups.　The　agricultural　section　contained　more　common　DOM　molecules　than　the　urban　section,　mainly　tannin-like　and　lignin-like　substances　with　unsaturated　or　cyclic　structures.　And,　the　intensity　of　anthropogenic　activities　was　the　main　reason　affecting　the　diversity　of　unique　DOM　molecular　in　each　sample.　Moreover,　Dechloromonas　as　the　dominant　genus　of　Proteobacteria　was　closely　related　to　the　biological　modification　of　low　unsaturated　(DBE　＜　15)　condensed　aromatic　compounds　(P　＜　0.05).　Anaerolineaceae　and　Anaerolineae　belonging　to　the　Chloroflexi　phylum　have　the　potential　to　degrade　medium　and　high　molecular　weight　(M/Z＞　400)　liable　substances　(P　＜　0.05)　and　release　lignin-like　substances.　In　addition,　the　proportion　of　protein-like　substances　can　indirectly　reflect　the　risk　of　nutrient　release　in　sediments　affected　by　urbanization.　Thus,　the　results　of　this　study　further　reveal　the　impact　of　urbanization　on　rivers,　and　provide　theoretical　basis　and　guidance　for　pollution　control　of　the　Beiyun　River　and　other　urbanized　rivers　worldwide.