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In this study, the microbial diversity in Tibetan flavor <i>Daqu</i> was analyzed based on single molecule real-time sequencing (SMRT). The volatile flavor compounds in <i>Daqu</i> were detected using the headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS). In addition, the correlation between various microbes and volatile flavor compounds was explored. Our studies indicated that the dominant bacterial genera in Tibetan flavor <i>Daqu</i> were <i>Oceanobacillus</i>, <i>Kroppenstedtia</i>, <i>Virgibacillus</i>, <i>Enterococcus</i>, <i>Pediococcus</i>, <i>Streptomyces</i>, <i>Saccharopolyspora</i>, <i>Leuconostoc</i>, <i>uncultured_bacterium_f_Lachnospiraceae</i> and <i>Lactobacillus</i>. The dominant fungal genera were <i>Wickerhamomyces</i>, <i>Monascus</i>, <i>Aspergillus</i> and <i>Rhizomucor</i>. 101 volatile compounds were detected in the <i>Daqu</i> samples, including alcohols, acids, esters, aldehydes, hydrocarbons, ketones, ethers, aromatics and pyrazines, and 10 key flavor compounds were identified using the relative odor activity value (ROAV). The results of our correlation analysis showed that <i>Enterococcus</i> was mainly associated with the synthesis of aldehydes such as trans-2-octenal, and <i>uncultured_bacterium_f_lachnospiraceae</i> was associated with the synthesis of most aldehydes. This paper has systematically investigated the physicochemical indices, microbial community structure and flavor compounds of Tibetan flavor <i>Daqu</i>, which is helpful in gaining a deeper understanding of the characteristics of Tibetan flavor <i>Daqu</i>.