The coastal wetland is easily invaded by alien species due to its location in the land and sea transitional area. As a potential driving regeneration force, the soil seed bank is vital to community restoration and species diversity protection. To reveal the long-term S. alterniflora invasion impact on the soil seed banks and regenerated communities, we investigated the seed banks under the different vegetation types (S. alterniflora, Phragmites australis, Scirpus mariquete, ruderal and unvegetated site) and soil depths (0–5 cm and 5–10 cm) in the Chongming island coastal salt marsh wetland. The results showed that the soil seed bank richness and species density under different vegetation types were higher than aboveground vegetation, and those of 0–5 cm seed banks were higher than 5–10 cm, except for the unvegetated site. The species richness and the S. alterniflora seed proportion in the seed banks under the S. alterniflora communities (S.AS) were lower and larger, respectively, than other sites. The species composition between S.AS and the aboveground communities showed high similarity with aggregation phylogenetic structures in two soil depths. The seed bank variations at 0–5 cm and 5–10 cm depths were interpreted 3.03% and 2.25% by aboveground communities, while 4.92% and 5.55% were interpreted by soil microbial biomass. The SEM model explained 98.1% and 91.8% of the seed banks' richness at the 0–5 cm depth and 5–10 cm depth, respectively, and explained 98.8% and 46.1% of the seed banks' species density at the 0–5 cm depth and 5–10 cm depth, respectively. The aboveground vegetation biomass and abundance directly affected the 0–5 cm seed banks' richness and species density, while its height and biomass only affected the 5–10 cm seed banks' species density. The microbial biomass of the 0–10 cm soil depth indirectly affected the richness and species density of the 0-5 cm seed bank, and only affected the richness of the 5–10 cm seed bank. Soil physical and chemical properties only indirectly affected the 0–5 cm seed banks' species density. The results provided a reference for the ecological evaluation of the impacts of S. alterniflora invasion into the coastal salt marsh wetland of eastern China and guidance for the protection and restoration of the native plant communities.