To elucidate the spatial-temporal impact of invasive saltmarsh plant Spartina anglica on the biogeochemical processes in coastal wetlands, we investigated the rates and partitioning of organic carbon (Corg) mineralization in three representative benthic habitats: (1) vegetated sediments inhabited by invasive S. anglica (SA); vegetated sediments by indigenous Suaeda japonica; and (3) unvegetated mud flats. Microbial metabolic rates were greatly stimulated at the SA site during the active growing seasons of Spartina, indicating that a substantial amount of organic substrates was supplied from the high below-ground biomass of Spartina. At the SA site, sulfate reduction dominated the Corg mineralization pathways during the plant growing season, whereas iron reduction dominated during the non-growing season. Overall, due to its greater biomass and longer growing season than native Suaeda, the expansion of invasive Spartina is likely to greatly alter the Corg-Fe-S cycles and carbon storage capacity in the coastal wetlands.