The microbial population structure in traditional fermentation food is complex and diverse, and studying the characteristics of microbial composition and metabolism in the fermentation process can reveal the relationship between the composition of microbial composition and metabolites, and thus better control the quality of fermentation foods. In this review, the evolution of microbial structure in typical Chinese traditional fermentation foods was summarized. Combined with the development of modern detection technologies, the structural composition of microorganisms in the fermentation foods and the evolution rules of the populations and the changing laws of metabolites were analyzed, as well as their important role in the search for the core functional microorganisms of traditional fermentation foods, and the development of fermentation food was also discussed.