Display omitted •LLE-GC–MS-based metabolomics was used to investigate the VOCs change during koumiss fermentation.•15 differential metabolites between mare’s milk and koumiss were confirmed.•The correlation between flavor formation and microbial community was established.•Lactobacillus and Dekkera were the most important flavor-producing microbiota.•The fatty acid synthesis pathway was focused from identified prominent pathways. Koumiss, naturally fermented mare’s milk, has a unique flavor that is affected by its resident microflora. In this study, we analyzed time-dependent changes in the microbiota and volatile metabolite profiles of koumiss using high-throughput sequencing and liquid–liquid extraction–gas chromatography–mass spectrometry. The dominant microrganisms in mare milk were Enterobacter and Rhodotorula, which were gradually suppressed, then Lactobacillus and Dekkera became the core microorganisms of koumiss. 17 FAA and 52 volatile organic compounds (VOCs) were identified during koumiss fermentation, including 19 odor active compounds and 15 differential metabolites of VOCs, mainly acids and esters, and their anabolism showed significant positive correlations with Lactobacillus and Dekkera. The microbial metabolic network showed that Lactobacillus and Dekkera were identified as the most important flavor-producing microbiota due to their significantly positive correlation with the formation of 33 and 28 flavor metabolites, respectively. These microorganisms produce enzymes that catalyze a series of metabolic pathways that generate VOCs, including carbohydrate metabolism, amino acid metabolism, and fatty acid biosynthesis. Our findings provide new guidance for the screening and application of flavor-producing microorganisms inkoumiss.