In order to explore the changes in the bacterial community structure and diversity in sea buckthorn jiaosu during natural fermentation, Illumina-MiSeq high-throughput sequencing technology was used to study the bacterial diversity of sea buckthorn jiaosu liquid at different fermentation stages. The results showed that a total of 601 species belonging to 422 genera, 239 families, 149 orders, 57 classes and 25 phyla were obtained by the analysis of operational taxonomic unit (OTU). Cyanobacteria, Proteobacteria, unclassified_k__norank_d__Bacteria, Acidobacteriota, Firmicutes were the five dominant phyla in sea buckthorn jiaosu. Among them, Cyanobacteria was the absolute dominant phylum and its relative abundance at three fermentation stages, namely F22_Q (72 h), F22_Z (624 h) and F22_H (1584 h) were 93.28%, 66.59% and 35.40%, respectively. Norank_f__norank_o__Chloroplast, Ralstonia, unclassified_k__norank_d__Bacteria, norank_f__Mitochondria, Burkholderia-Caballeronia-Paraburkholderia were the dominant genera. Among them, norank_f__norank_o__Chloroplast was the absolute dominant genus and its relative abundance ranged from 35.39% to 93.28%. The three fermentation stageswere clustered into two groups by sample cluster analysis and principal component analysis (PCA); one group consisted of the early stage (F22_Q) and middle stage (F22_Z), and the other group consisted of the late stage (F22_H). The results from this study could provide a theoretical basis for sea buckthorn jiaosu fermentation.