Abstract: To explore the regime shift of soil microbial community structure after Spartina alterniflora invasion, four soil samples were collected from mudflats with and without S. alterniflora in Beibu Gulf, Guangxi. 16S rDNA was used to analyze the differences in soil microbial community composition and diversity. Canonical correspondence analysis was used to study the correlation between soil microorganisms and soil physio-chemical characteristics. The results showed that the rank of dominant species of soil microbial community changed after S. alterniflora invasion in the mudflat of Beibu Gulf, Guangxi. The top five phylum in abundance were Proteobacteria > Acidobacteria > Chloroflexi > Acinobacteria > Bacteroidetes. Among them, the indicator species of S. alterniflora, i.e., Chloroflexi increased from the top fourth to the third. Soil microbial diversity fluctuated significantly. CCA analysis showed that soil salinity and humidity were the main factors affecting the regime shift of microbial community after S. alterniflora invasion (P < 0.05).