Abstract: In this study, the microbial community composition of Shanxi vinegar fermentation was analyzed through high-throughput sequencing, and the changes of microbial community in the two major fermentation stages of alcoholic fermentation and acetic acid fermentation were investigated. The results showed that Firmicutes and Proteobacteria were the main phyla in Cuqu (R1), alcoholic fermentation (R2) and acetic acid fermentation (R3) for the bacterial community structure. The dominant genus in R1 was Weissella. In R2, the dominant genus was Weissella at the beginning, and gradually Lactobacillus dominated at the later stage of fermentation. The dominant genus in R3 was changed from the initial Lactobacillus to Acetobacter. For the fungal community structure, the main phyla in R1, R2 and R3 were Ascomycota and Basidiomycota, and the dominant genera in R1 were Issatchenkia, Aspergilus and Millerozyma. In R2, Issatchenkia was the absolute dominant genus, which was on the rise at this stage. In R3, Issatchenkia was still the dominant genus and showed a first rise and then a decline at this stage, with the highest relative abundance reaching 81.3%. There were six genera with significant differences between R2 and R3, namely Staphylococcus, Bacillus, Enterococcus, Leuconostoc, Geobacillus and Aspergillus. In conclusion, the microbial community structure of Shanxi vinegar in different fermentation stages was different and changed with the fermentation.