In this study, the bacterial community structure and diversity in five samples of bacteria-fermented Sojae Semen Praeparatum produced in different areas of Enshi Prefecture were investigated using high-throughput sequencing on the Illumina PE250 platform. The results showed that the microbial composition of Sojae Semen Praeparatum was diverse. A total of 17 phyla, 24 classes, 43 orders, 78 families, 152 genera and 93 species were identified. Among them, the core dominant phylum were Firmicutes, followed by Proteobacteria, Cyanobacteria and Actinobacteria. The dominant genera were Bacillus thermoamylovorans and Bacillus smithii. The composition of dominant genera in the five samples was the same, but the relative abundance was quite different. There was a significant difference in the composition and relative abundance of the other minor genera.