A Spartina alterniflora tidal flat(HH),(coverage 25%-30%) and a natural tidal flat(ZR) were studied to determine the impact of a S. alterniflora invasion on the vertical structure of a macrobenthic community. Macrobenthos field sampling was carried out in the HH and ZR areas in Xuanmen Bay National Wetland Park, YuHuan County, Zhejiang Province, China, in August 2012. The tidal flat was reclaimed in 2005 and its current width is approximately 200-250 m. The study area was divided into HH and ZR habitat types, which are defined by geomorphological features and vegetation distribution. Within each habitat type, three sample lines were selected. Each sample line was composed of five sites, which were 50 m, 100 m, 150 m, 200 m, and 250 m from the coast. Four quadrats(25×25×25 cm) were taken from independent patches in each site and sieved(1 mm). Macrobenthos samples were collected from depths of 0 cm, 0-5 cm, 5-10 cm, 10-15 cm, 15-20 cm, and 20-25 cm, with a newly designed, stratified macrobenthos sampling device. We analyzed the numerical data using several biodiversity indices, e.g., the Shannon-Wiener(H'), Pielou(J), Margalef(D_ma), and Simpson(D) indices. Community structure was determined by hierarchical cluster and multidimensional scaling analyses. Significance testing for differences in macrobenthic species and density between sample lines and sediment depth was undertaken. Based on the data collected from three sample lines in the ZR and three in the HH, a total of 40 species were obtained, of which 18 species were Mollusca, 13 were Crustacea, 4 were Polychaeta, and the remaining five were members of various other taxonomic groups. Thirty species were obtained in the ZR, 31 were obtained in the HH, and 21 were found in both habitats. In both HH and ZR, the macrobenthic species numbers were highest at 0-5 cm depth and lowest at 20-25 cm depth. The average density in the HH and ZR was 222.6 ind./m²and 1052.8 ind./m², respectively. The main habitat depth coincidence rate was more than 50% when the quantities of species were more than 1% of the total species. When the quantities of species were more than 10% of the total species, then the coincidence rate was more than 75%. In the 0-20 cm deep HH sediment, the Margalef, Shannon-Wiener, and Pielou indices were higher than at the same sediment depth in ZR, but the Simpson index showed an opposite trend. In the 20-25 cm deep HH sediment, the Margalef, Shannon-Wiener, and Pielou indices were lower at the same depth in ZR. Again, the Simpson index showed an opposite trend. The results revealed that(1) In HH and ZR, macrobenthos mainly inhabit the 0-10 cm deep sediment category;(2) different macrobenthic communities are distributed at different sediment depths in both habitats;(3) the invasion of S. alterniflora reduced the vertical macrobenthos distribution depth, but had little effect on its main habitat depth; and(4) the S. alterniflora invasion altered the original habitat characteristics, which caused changes to the macrobenthic community structure.