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As a typical invasive species, <i>Spartina alterniflora</i> is widely recognized as one of the primary threats to biodiversity in various habitats, including wetlands. Although the invasion by <i>S. alterniflora</i> has been managed in multiple ways, it may reappear after treatment. How <i>S. alterniflora</i> affects the soil microbial community in coastal wetlands during its regeneration process has not yet been clarified. Here, rhizosphere soil samples (RSPs) and bulk soil samples (SSPs) were collected in the <i>S. alterniflora</i> community and a high-throughput sequencing method was conducted to analyze the composition and diversity of soil microorganisms. Meanwhile, we also obtain the soil physicochemical properties. In the present study, there was no significant difference in the alpha diversity of both bacterial and fungal communities in the SSP and RSP groups. The PCoA (principal coordinate analysis) also showed that the microbial community structure did not differ significantly between the SSP and RSP groups. The results showed that except for pH, the total sulfur (TS) content, total nitrogen (TN) content, and electrical conductivity (EC) did not differ significantly (<i>p</i> > 0.05) between the SSP and RSP groups. The composition of the bacterial and fungal community in the rhizosphere of <i>S. alterniflora</i> was similar to that found in the surrounding soils. The top two dominant bacterial phyla were Proteobacteria and Desulfobacterota in the present study. Venn diagram results also support this view; most OTUs belong to the common OTUs of the two groups, and the proportion of unique OTUs is relatively small. The LEfSe (LDA effect size) analysis showed that Campylobacterota (at the phylum level) and <i>Sulfurimonas</i> (at the genus level) significantly increased in the RSP group, implying that the increased <i>Sulfurimonas</i> might play an essential role in the invasion by <i>S. alterniflora</i> during the under-water period. Overall, these results suggest that the bacterial and fungal communities were not significantly affected by the <i>S. alterniflora</i> invasion due to the short invasion time.