To explore the effects of microbial community changes on the key flavor substances in base Baijiu, this study analyzed the microbiome of the pre-pit fermentation grains using high-throughput sequencing technology and determined the flavor substances of the base Baijiu by GC-FID. The results showed the microbial community changed dynamically between the different rounds, as well as bacteria and fungi displayed different succession patterns. Next, the variations of skeletal flavor substances in the base Baijiu were analyzed by multiomics, and it was found that alcohols, acids, and esters were the most abundant, accounting for 88.16–98.87% of the total flavor substances, and decreased with the increase of the rounds. By calculating the Spearman coefficient, it was found that microorganisms such as Acinetobacter, Oceanobacillus, Saccharomyces, and Byssochlamys were significantly correlated with the n-Propano and 2,3-Butanediol and other components in the base Baijiu. Finally, 15 flavor substances such as Acetaldehyde, Propionaldehyde, and Isobutyraldehyde were identified as key substances by OAV analysis. This study is the first to reveal the potential association between the microbial community of pre-pit fermentation grains and flavor of base Baijiu and has the benefit of improving the quality of base Baijiu.

Jiaomian base baijiu is an important seasoning liquor used in the blending of sauce-flavor baijiu, yet the mechanism underlying its flavor formation remains insufficiently understood. Moreover, the specific contribution of high-temperature Daqu (HTDQ) to the flavor profile of Jiaomian base baijiu has not been clearly defined. Therefore, this study compared the aroma profiles and flavor compounds of Jiaomian and Chuntian base baijiu. Jiaomian base baijiu displayed stronger Qu-aroma and floral–fruity notes, with six differential flavor markers (VIP > 1) identified, including ethyl acetate, acetaldehyde, and n-propanol. Further analysis showed that yellow HTDQ exhibited greater inner–outer heterogeneity in aroma and flavor profiles than white and black HTDQ. It also contained the highest concentration of flavor compounds and exerted the strongest influence on the flavor of Jiaomian base baijiu. By comparing the flavor compounds of HTDQ and base baijiu, 14 key compounds were identified that mediate the influence of HTDQ on the flavor of Jiaomian base baijiu. These compounds were primarily formed during the early to middle stages of HTDQ fermentation. Correlation analysis further indicated that microorganisms during HTDQ fermentation were predominantly positively correlated with the key flavor compounds. Among them, Thermoactinomyces, Byssochlamys, Kazachstania, Leiothecium, and Trichothecium showed the closest associations—positively correlated with compounds such as 1-nonanol and furfuryl alcohol, and negatively correlated with isovaleric acid. Finally, KEGG enrichment analysis of the flavor compounds suggested that Beta Oxidation of Very Long-Chain Fatty Acids, Mitochondrial Beta-Oxidation of Short-Chain Saturated Fatty Acids, and Fatty Acid Biosynthesis are key pathways involved in the formation of these flavor substances. In summary, this study clarifies the key flavor compounds through which different HTDQ types influence base baijiu flavor, reveals the microbial origins and metabolic pathways of these key flavor compounds, and provides a theoretical basis for regulating HTDQ production and improving the quality of base baijiu.