<p>Microplastics (MPs) in river ecosystems significantly affect sediment microbial communities and biogeochemical cycling. However, the specific microbial responses to distinct MPs and their subsequent effects on greenhouse gas (GHG) emissions remain poorly understood. In this study, the effects of conventional polyvinyl chloride (PVC) and biodegradable polylactic acid (PLA) on sediment microbial communities and GHG emissions were compared. Both PVC and PLA increased sediment total organic carbon (STOC) by 31.3% and 36.7%, respectively, leading to an increase in sediment bacterial abundance. Notably, compared with PLA, PVC reduced bacterial richness more significantly. Community composition and FAPROTAX function prediction analysis revealed that PVC-enriched taxa involved in nitrate reduction (e.g., <i>Desulfuromonas</i>, <i>Hydrogenophage</i>, <i>Azospira</i>) resulted in a significant decrease in NO₃⁻ contents. In contrast, PLA increased the abundance of microorganisms associated with organic matter degradation (<i>Chitinophagaceae</i>, <i>Comamonadaceae</i>, and <i>Caulobacteraceae</i>). Both PVC and PLA significantly reduced the relative abundance of the <i>mcr</i>A gene, leading to decreased CH₄ fluxes, likely due to competition from enriched acetate-utilizing bacteria (<i>Desulfuromonas</i>, <i>Pseudomonas</i>, and <i>Azospira</i>). Additionally, PLA significantly reduced the abundance of the <i>nir</i>K gene. This study systematically elucidates the differential effects of PVC and PLA on microbial community structure and GHG emissions, providing new insights into the ecological impacts of MPs.</p>