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Xiaoqu is a fermentation starter used in the production of Xiaoqu jiu, which is also a traditional Chinese liquor. The quality and microbial community characteristics of Xiaoqu is closely related with the yield and flavor feature of fresh Xiaoqu jiu. The present study aims to explore the mystery behind microbial diversity and volatiles of Xiaoqu through polyphasic detection methods such as the Illumina MiSeq platform and the metabolite analyzing method. Results showed that differences in microbial community diversity among samples were significant. The hydrolytic ability was positively correlated with α- and β-diversity of bacteria, but negatively correlated with that of fungi. Staphylococcus and Weissella were the dominant bacteria, while Rhizopus and Candida were the dominant fungi. The abundance of bacteria in sample No3 ranged from 33.66 to 91.53%, while sample No4 the abundance of fungi ranged from 58.51 to 48.72%. The difference of microbial community diversity resulted in a discrepancy of volatile profiles and interaction relationship among the genus. Twenty-four dominant bacteria and seven dominant fungi were correlated with 20 different volatiles. This study provides a scientific perspective of the uniformity and stability of Xiaoqu jiu and might aid in controlling its manufacturing process.