The exotic smooth cordgrass (Spartina alterniflora) has invaded intertidal wetlands near the Ronggenshan tidal flats of Beihai, Guangxi, China, where historically seagrasses and mangroves coexisted. We investigated sediment organic carbon (SOC) storage and macrobenthic community structure in the existing mangroves (MG), S. alterniflora (SA), seagrass bed (SG), and unvegetated flat (UnV) habitats following the S. alterniflora invasion. SOC storage increased after S. alternifolia invasion in the SG and UnV habitats. Spartina alterniflora invasion changed the dominant species of the macrobenthos in the original habitats and reduced the diversity of macrobenthos in SG and UnV habitats. Clearly, S. alternifolia invasion can change the ecological functioning of south China's coastal ecosystems by altering carbon sequestration and affecting biodiversity.