In order to comprehensively explore the regulatory effect of bioturbation on the assembly and overall metabolic characteristics of Daqu microbial community. This study used metatranscriptomics and metabolomics to investigate the composition of the microbial community, physicochemical properties, and overall metabolic profile of Daqu before and after bioturbation by Bacillus velezensis. The results demonstrated that the acidity, moisture, amino acid nitrogen, and starch content of Daqu exhibited a significant increase following bioturbation. The symbol microorganisms of Daqu have also changed significantly, from the original Aspergillus chevalieri, Rasamsonia emersonii, Aspergillus ruber, Aspergillus glaucus, Aspergillus wentii and Aspergillus cristatus to Paecilomyces varioti, Trichomonascus ciferrii and Staphylococcus gallinarum. Correlation analyses and integration pathways indicated that altered microbial community abundance also promoted the metabolism of starch, ethanol, fatty acids, and pyrazine, resulting in a significant enhancement of Daqu's saccharification and liquefaction power, as well as the content of some volatile and non-volatile metabolites, with pyrazines increased by 24.50%. The application of fortified Daqu to Baijiu fermentation can significantly enhance the content of various pyrazines in Baijiu. These results are helpful to elucidate the mechanism of biochemical changes, microbial assembly and flavor production of Daqu after biodisturbance.