Storage is a crucial step in the production of Daqu, but the microbiological and flavor chemical kinetics of the storage process remain largely unknown and limit the quality control of Daqu. In this study, the microbial communities and volatile compounds were analyzed and compared during the storage of Daqu. Virgibacillus, Bacillus and Kroppenstedtia were the dominant bacterial genera, and Thermoascus, Thermomyces and Aspergillus were the dominant fungal genera. By LEfSe analysis, JW1 Daqu had more differential microbial markers. At the end of storage, the content of some compounds decreased significantly, such as esters, alcohols and ketones. In addition, PICRUSt2 predicted enzymes related to some important aroma production. These results indicated that microbial communities and volatiles changed significantly during storage of Daqu, which might be important for optimization of quality.