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The Chishui River basin is the main production area of the sauce-flavor Baijiu. Due to the particularity of sauce-flavor Baijiu technology, a large site of workshops needs to be built for brewing and storage. Therefore, used the natural karst caves of Guizhou province to manufacture the sauce-flavor Baijiu, which has enriched the connotation of sauce-flavor Baijiu and saved valuable land resources. In this study, the fermentation grains in the seven stages during the Xiasha round of the cave-brewed sauce-flavor Baijiu (CBSB) were detected using a combination of physicochemical analysis, Headspace solid-phase microextraction gas chromatography-mass detection, and Illumina HiSeq sequencing methods. The results showed Unspecified_Leuconostocaceae, Weissella, Unspecified_Bacillaceae, Saccharomycopsis, Thermomyces, and Unspecified_Phaffomycetaceae were the main bacterial and fungal genera in the stacking fermentation (SF). In the cellar fermentation (CF), the Lactobacillus, Unspecified_Lactobacillaceae, Thermoactinomyces, Saccharomycopsis, Unspecified_Phaffomycetaceae, and Wickerhamomyces were the main bacterial and fungal genera. A total of 72 volatiles were detected in the fermented grains. Linear discriminant analysis Effect Size (LEfSe) identified 23 significantly different volatile metabolites in the fermentation process, including 7 esters, 6 alcohols, 4 acids, 3 phenols, 1 hydrocarbon, and 2 other compounds. Redundancy analysis was used to explore the correlation between dominant microbial genera and physicochemical properties. Starch was the main physicochemical property affecting microbial succession in the SF. Acidity, moisture, and reducing sugar were the main driving factors of microbial succession in the CF. The Pearson correlation coefficient revealed the correlation between dominant microbial genera and significantly different volatile flavor substances. A total of 18 dominant microbial genera were associated with significantly different volatile metabolites, Lactobacillus, Weissella, Wickerhamomyces, and Aspergillus were shown to play crucial roles in metabolite synthesis. On this basis, a metabolic map of the dominant microbial genera was established. This study provides a theoretical basis for the production and quality control of sauce-flavor Baijiu brewed in natural karst caves and lays a foundation for studying the link between flavor formation and microorganisms.