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A Qingzhi compound-flavor Baijiu (QZCF Baijiu) was developed and the physiochemical factors and microbial community structure in Jiupei (fermented grains) during Baijiu fermentation were revealed. Physiochemical factors of ethanol, moisture and acidity significantly increased in the fermentation, while starch and reducing sugar decreased. The results of high-throughput sequencing showed that Weissella, Pediococcus, Bacillus, Pantoea, Streptococcus, Sphingobacterium, Saccharomyces, Rhizopus, Issatchenkia and Wickerhamomyces were the dominant microorganisms in Jiupei. Moreover, correlation analysis between the physicochemical factors, the dominant microorganisms and the important flavor compounds in QZCF Baijiu production highlighted that the changes of physiochemical factors would lead to the corresponding changes of core microbiota and important flavor substances. Physiochemical factors of starch, reducing sugar and temperature could significantly affect the microbial community structure at the early stage of fermentation, while the influences of ethanol content and acidity became greater at the later stage, resulting in the differences of flavor compounds in Jiupei. Therefore, the growth and metabolism of microbial communities could be regulated by purposefully adjusting the physiochemical factors, thereby improving the flavor and quality of Baijiu. This work enriched the flavor types of Baijiu and provided a reference for the Baijiu-making industries to manage their production process.