To ensure quality stability of strong-flavor Daqu (SFD)—a key saccharification starter in Baijiu production—this study investigated the dynamic succession of fungal communities during fermentation and storage. Using high-throughput sequencing of samples from two production regions, we characterized changes in fungal communities and Physiochemical properties. Predominant genera included Clavispora, Wickerhamomyces, Dipodascus, Thermomyces, Candida, Geotrichum, Aspergillus, and Thermoascus. Correlation analysis revealed significant associations (P < 0.05) between saccharification power and six genera (e.g., Rhizopus and Blastobotrys), and between liquefaction power and four genera (e.g., Millerozyma and Lichtheimia). This study elucidates the dynamic succession of the fungal community during the fermentation and storage of SFD, clarifying the relationship between the fungal community and physicochemical properties.

NongXiangXing Baijiu (NBJ) is produced using a solid-state fermentation system, but the impact of stratified fermented grains on fermentation remains unclear. Therefore, in a typical distillery plant, we evaluated the physical and chemical composition, volatile compound profile, and microbial community of fermented grains in NBJ both above (FG-A) and below (FG-B) the Huangshui line. Significant differences in fermentation parameters between FG-A and FG-B were observed after 30 days of fermentation (P < 0.05). Additionally, the partial least squares projection to latent structure discriminant analysis (PLS-DA) revealed distinct differences in volatile compounds between FG-B and FG-A, identifying 26 discriminant markers. The diversity of short-chain fatty acids (SCFAs) and their esters was higher in FG-B compared to FG-A. Furthermore, microbial diversity and abundance differed significantly between the two layers of fermented grains (P < 0.05). Correlation and pathway enrichment analyses indicated that the higher SCFA content in FG-B could be attributed to the greater abundance of acid-producing microorganisms compared to FG-A. This study highlights the differences between the two layers of fermented grains in NBJ fermentation, offering new insights into solid-state fermentation and expanding the current understanding of the traditional NBJ fermentation process.