Abstract: In order to explore the correlation between physicochemical indexes, volatile flavor and microbial diversity during the fermentation of red millet Huangjiu, high throughput sequencing of microorganisms, physicochemical index detection and gas chromatography-mass spectrometry were used and SPSS software was applied for correlation analysis. The results showed that during the progress of fermentation, the content of reducing sugar decreased rapidly at first and then became stabilized gradually, while the trend of alcohol content was opposite; the content of total acid increased rapidly in the early stage, then decreased and finally increased again, while the pH value stayed at a same level; the alteration of amino acid nitrogen level was volatility rised in the beginning and then increased fast, while soluble solids content first declined quickly and then kept stabilized. A total of 14 bacterial phyla and 228 bacterial genera, 7 fungal phyla and 108 fungal genera were detected in 10 stages (1~7, 10, 20, 30 days) during fermentation. At the genus level, the bacterial community could be clustered in 3 types, and the fungal community could be clustered in 5 types. Bacteria genus levels were positively correlated with total acid (P<0.05) while negatively correlated with reducing sugar (P<0.05), and fungi genus levels were positively correlated with amino nitrogen (P<0.05). 2,3-Butanediol and ethyl lactate were positively correlated with most of the bacteria (P<0.05). Klebsiella was negatively correlated with ethyl octanoate (P<0.05), while Lactococcus was negatively correlated with ethanol, 2-butanol, isobutanol, phenylethanol and ethyl palmitate (P<0.05). Monascus was significantly negatively correlated with ethyl lactate (P<0.05), while Apiotrichum was negatively correlated with 2-butanol, isobutanol and isoamyl alcohol (P<0.05). Our results indicated that the microbial diversity significantly changed during the fermentation of red millet Huangjiu, which had a certain correlation with the physicochemical indicators and flavor variations. These findings provided a theoretical reference for the subsequent study on quality improvement and deve-lopment of red millet Huangjiu.