Benthic macrofaunal community structure was related to vegetation and sediment properties along a low to high marsh elevational gradient in Scirpus mariqueter marsh on the eastern coast of Chongming Island in the Changjiang estuary, China. Multivariate analysis indicated that there were significant differences in macrofaunal community structure between the marsh zones sampled. There were positive relationships between attributes of salt marsh vegetation and macrofaunal community. The main factors explaining macrofaunal community structure along the habitat gradient were shoot height and below-ground plant biomass. In the Scirpus mariqueter marsh studied, above-ground and below-ground plant structure formed a complex habitat, adding structural heterogeneity to the surface sedimentary environment. Habitat heterogeneity is important for supporting diverse macrofaunal assemblages.