To explore the mechanism of the stack fermentation process in Taorong-type Baijiu brewing, this study collected fermented grain (Jiupei) samples at different stacking stages for analysis of the microbial community structure and dynamic changes during the stack fermentation process using the Illumina MiSeq high-throughput sequencing platform. Gas chromatography-mass spectrometry (GC-MS) was used to characterize the flavor compounds in Jiupei, and redundancy analysis (RDA) combined with Spearman correlation coefficients was applied to assess the correlations of physicochemical factors and flavor compounds with microbial communities. The results showed that Firmicutes was the dominant bacterial phylum throughout the stack fermentation process, with the relative abundance of Bacillus reaching its peak (63.47%) at 24 h. The fungal community was primarily composed of Ascomycota; Wickerhamomyces-Candida_clade was more abundant in the early stage (0-12 h), while the relative abundance of Pichia increased continuously with stacking time. Starch was identified as the key physicochemical factor influencing microbial succession during the fermentation process. Furthermore, correlation analysis revealed that the fungal genus Wickerhamomyces-Candida_clade exhibited significantly negative correlations with alcohols and esters (P < 0.05), whereas the bacterial genus Weissella showed significantly positive correlations with these flavor compounds (P < 0.05). Notably, Bacillus was strongly negatively correlated with acids (P < 0.01). These findings provide a theoretical foundation for further elucidating the fermentation mechanism of Taorong-type Baijiu.