Abstract: In order to reveal the evolution of bacterial flora during the natural fermentation process of sea buckthorn jiaosu, changes in the bacterial community structure of fermentation were analyzed by Illumina Miseq high-throughput sequencing technique. Moreover, changes in physicochemical indexes and active components were also monitored. The results showed that after 60 days of natural fermentation, pH decreased from 4.42 to 3.47, total acid increased from 2.6 g/L to 10.54 g/L, total sugar decreased from 80.69 g/L to 32.59 g/L, and soluble protein decreased from 0.87 g /L decreased to 0.28 g/L, while total flavonoids and total polyphenols increased from 0.11 g/L and 1.24 g/L to 0.47 g/L and 4.55 g/L, respectively. A gradual decline trend in species diversity of the bacterial community was observed during the sea buckthorn jiaosu fermentation. Firmicutes and Proteobacteria were detected as the main advantage phylum during the whole fermentation process, and the sum of their relative abundance was greater than 97%. Lactobacillus was the absolute dominant genus in the late fermentation stage, and its relative abundance was reached 82.16% after 60 days of fermentation. In addition, the results of redundant analysis showed that pH and total acid content were found to be the main driving force of microbial community succession during the fermentation process of sea buckthorn jiaosu. This research may deepen the understanding of the mechanism in nature fermentation of sea buckthorn jiaosu, and provide a scientific basis for screening potentially valuable probiotics and realizing precise artificial regulation .