Soil microorganisms are important in maintaining the basic structure and function of ecosystems. To explore the characteristics of soil microbial community structures in Yancheng coastal wetlands, soil samples of mudflat and typical plant communities of Spartina alterniflora, Scirpus triqueter, Suaeda salsa, Phragmites australis were collected. In this study, 16S rRNA high-throughput sequencing technology was used to investigate the diversity and structure of soil microbial communities at the depth of 0-10 cm (surface layer), 10-30 cm (middle layer), and 30-60 cm (deep layer). The results indicated that: (1) there existed some differences in soil microbial composition among plant communities, especially for the structures of bacterial community. The differences between mudflat and plant communities in soil bacterial species composition and relative abundance, and the differences in bacterial species composition between soils of Spartina alterniflora community and those of native species, were much more. (2) The microbial community structures of different soil depths in the same community were similar, with differences less than among different communities. the significant soil microbial diversity differences existed in the five communities in surface-layer and deep-layer, but not in the middle-layer. Overall, plant species had greater effects on soil microbial community structure than soil depth. Compared with native plant communities, the species of soil microbial dominant phyla in Spartina alterniflora community had little difference, but the relative abundances of some dominant phyla changed significantly, with differences in the functional groups of microbial communities.