For four decades, cordgrass (Spartina alterniflora) has invaded salt marshes in the Yellow Sea, altering physical, biogeochemical, and biological processes. Here, we investigated the ecological effects of S. alterniflora invasion on benthic environments compared to native halophytes. S. alterniflora contributed to higher carbon accumulation rates compared with bare tidal flat in sediments (3.4 times), through greater primary production and root biomass, compared to Suaeda japonica (2.5 times) and Phragmites australis (2.4 times) over the given period. The results showed that S. alterniflora eradication treatments inhibited its growth but did not significantly affect the benthic communities. Compared to P. australis and bare tidal flats, S. alterniflora invasion resulted in lower greenhouse gas emission and higher contributions to macrobenthos nutrition, and increased sediment stability and carbon burial. Overall, these multiple lines of evidence provide new insights on S. alterniflora invasion, suggesting that the current eradication policy would be carefully reviewed.