Sauce-flavor Baijiu is representative of solid-state fermented Baijiu. It is significant to deeply reveal the dynamic changes of microorganisms in the manufacturing process and their impact on the formation of flavor chemicals correlated with the quality of Baijiu. Sauce-flavor Baijiu manufacturing process can be divided into seven rounds, from which seven kinds of base Baijius are produced. The quality of base Baijiu in the third round is significantly better than that in the first and second rounds, but the mystery behind the phenomenon has not yet been revealed. Based on high-throughput sequencing and flavor analysis of fermented grains, and correlation analysis, the concentrations of flavor chemicals in the third round of fermented grains were enhanced, including esters hexanoic acid, ethyl ester; octanoic acid, ethyl ester; decanoic acid, ethyl ester; dodecanoic acid, ethyl ester; phenylacetic acid, ethyl ester; 3-(methylthio)-propionic acid ethyl ester; acetic acid, phenylethyl ester; hexanoic acid, butyl ester, and other flavor chemicals closely related to the flavor of sauce-flavor Baijiu, such as tetramethylpyrazine. The changes in flavor chemicals should be an important reason for the quality improvement of the third round of base Baijiu. Correlation analysis showed that ester synthesis was promoted by the bacteria genus Lactobacillus and many low abundances of fungal genera, and these low abundances of fungal genera also had important contributions to the production of tetramethylpyrazine. Meanwhile, the degrading metabolic pathway of tetramethylpyrazine was investigated, and the possible microorganisms were correlated. These results clarified the base Baijiu quality improvement of the third round and helped to provide a theoretical basis for improving base Baijiu quality.