The microbial community diversity during the fermentation process of digital high-temperature Daqu and traditional high-temperature Daqu was analyzed by high-throughput sequencing on the Illumina MiSeq platform. Meanwhile, correlation analysis and bioinformatics analysis were conducted based on microbial species information and physicochemical properties. The results showed that the microbial community structure of high-temperature Daqu significantly changed during the fermentation process. At the end of fermentation, the major bacterial genera in high-temperature Daqu were Kroppenstedtia, Saccharopolyspora, Bacillus, Thermomyces, and Lactobacillus, and the major fungal genera were Thermoascus, Thermomyces, and Aspergillus. The results of non-metric multidimensional scale (NMDS) analysis and hierarchical clustering analysis (HCA) showed that the microbial community composition of the two types of Daqu was roughly similar at the same time points of fermentation.