Abstract: Objective: The aim of this study is to investigate the dynamics of microbial community structure and function during the natural fermentation process of sea buckthorn ferment at different stages using metagenomic analysis techniques. Methods: Genomic DNA extraction, PCR amplification, and purification were carried out on samples collected from fermentation process of sea buckthorn ferment at 10, 20, 30, 40d 50, and 60 d. Subsequently, Illumina PE library construction and metagenomic sequencing were performed to analyze the microbial community structure during the fermentation process of sea buckthorn ferment. Functional gene annotation and differential analysis were conducted by comparing with three databases: EggNOG, KEGG and CAZy. Results: The microbial communities exhibited high diversity and abundance throughout the different stages of fermentation process of sea buckthorn ferment. A comprehensive analysis revealed the presence of 48 phyla, 106 classes, 222 orders, 438 families, 881 genera, and 1561 species of microorganisms. Notably, Lactobacillus sp. (33.03%) and Pichia kudriavzevii (89.06%) dominated in the early stage of fermentation.Gluconobacte japonicus (40.3%) and Pichia kudriavzevii (71.12%) were prevalent in the middle stage, while Gluconobacter japonicus (35.71%) and Candida parapsilosis (66.01%) were dominant in the late stage. Prior to fermentation, annotated metabolic pathways primarily involved carbohydrate metabolism and amino acid. Metabolism with a total of 1628 genes related to energy formation and conversion, 2654 genes associated with amino acid metabolism, and 2275 genes involved in carbohydrate transport and metabolism. The most annotated metabolic pathways during the mid-fermentation stage are those related to coenzyme factors and vitamin metabolism, with a total of 2629 genes involved in translation, rRNA structure and synthesis, as well as 1692 genes involved in post-translational modification and protein folding. Throughout the entire fermentation period of sea buckthorn ferment, glycosyltransferase and glycoside hydrolase were the main enzyme in the entire fermentation cycle of sea buckthorn ferment. Conclusion: This study elucidates the variations in microbial community structure and function of sea buckthorn ferment at different fermentation stages, thereby providing a scientific foundation for further comprehensive research on the ecological composition and dynamic changes of its microbial community.