Daqu is the natural starter for Nong-flavor Baijiu brewing. The effects of Daqu properties on the microbial community succession and their metabolites in fermented grains (FG) during Baijiu brewing were determined. These results showed the effect of Daqu on the bacterial communities was stronger than that of the fungal communities. Compared with the conventional Daqu (DZ), Taikong (TK), and Qianghua (QH) Daqu significantly enhanced the content of volatile metabolites (especially esters) and ethanol when they were used, respectively, for FG fermentation. In the 2nd round of fermentation, the relative abundance of Lactobacillus decreased, the content of lactic acid decreased, and that of caproic acid increased. In particular, the abundance of Lactobacillus was also reduced by 20% in FGs of the 2 nd round when TK Daqu was used than that in the respective 1st round. PLS-SEM analysis also showed that physicochemical parameters and Daqu properties significantly affected FG community structure and metabolism. This study provides a theoretical basis for further study on the effect of high-quality Daqu on the quality of fresh Baijiu. and lays an important theoretical foundation for the stabilization of the Baijiu fermentation system based on Daqu.