Objective Optimization of Xiaoqu varieties in Guangxi for brewing rice-flavored Baijiu.Methods High-throughput sequencing was used to analyze the microbial communities of four Guangxi rice flavored Baijiu Xiaoqu, the physicochemical indexes of Xiaoqu were determined by the conventional methods, then the correlation between physicochemical indexes and the microbial communities was clarified.Results Two dominant fungal phyla and nine dominant bacterial phyla were detected in four Xiaoqu samples. The dominant fungal phyla were Ascomycota and Mucoromycota. As the dominant phyla of bacteria, Firmicutes and Proteobacteria are present in all Xiaoqu. Mould was found in all Xiaoqu samples, namely, Rhizopusa was found in Xiaoqu A, B, and C, and Aspergillus and Monascus were found in Xiaoqu D. The common dominant bacterial genera are Pediococcus and Weissella. In terms of physicochemical indexes, the saccharification power, liquefaction power and fermentation power of Xiaoqu A were all the biggest, while the esterification power of Xiaoqu C was greater than that of the other three Xiaoqu.Conclusion There is a certain correlation between relevant microorganisms and physicochemical indexes.