Abstract: In order to clarify the differences in the community structure and gene function of medium-high temperature Daqu bacteria in Linyi, Shandong Province and Zhoukou, Henan Province. MiSeq high-throughput sequencing technology was used to analyze the bacterial community structure of medium-high temperature Daqu in the two regions, and the potential functions of bacterial taxa were analyzed based on the clusters of orthologous groups of proteins (COG). The result of α diversity showed that there were no significant differences in richness and diversity (P>0.05). Compared with Daqu in Zhoukou area, at the phylum level, the average relative abundance of Actinobacteria and Bacteroidetes in Daqu in Linyi area were significantly lower (P<0.05). At the genus level, the average relative abundance of Acinetobacter was significantly higher (P<0.05), and the average relative abundance of Geobacter and Pantoea were significantly lower (P<0.05). The result of linear discriminant analysis effect size (LEfSe) showed that Geobacter was a biomarker in Zhoukou area Daqu, while the biomarker in Linyi area Daqu was not reflected at the genus level. The result of β diversity showed that there were obvious differences as a whole. The result showed that Daqu in Linyi area was significantly higher than Daqu in Zhoukou area in transcription, amino acid and nucleoside transport and metabolic functions by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) (P<0.05). Thus, there are obvious differences in bacterial community structure and gene function expression in the two regions.