Composition structure and differences of bacteria and fungi of Fenjiu Fu-qu and Dong-qu in different periods and regions were analyzed by high-throughput sequencing. The results showed that a total of 850 bacterial operational taxonomic units (OTU) and 233 fungal OTU were obtained, among them, including 54 bacterial core OTU and 15 fungal core OTU. The composition of dominant microorganisms in different Daqu was similar, the dominant bacteria genera were Pantoea, Enterobacter, Lactobacillus, Staphylococcus, Bacillus, and Weisella, etc., and the dominant fungi genera were Pichia and Saccharomycopsis. However, the abundance of these dominant microorganisms varied greatly in the different Daqu, especially Fu-qu with obvious characteristics, which had the highest abundance of Lactobacillus and Pichia, laying biological foundation for the high quality, stability and high yield of Fenjiu.