Liuyang Douchi is a kind of traditional fermented Aspergillus-type Douchi in China for excellent favor. However, studies on the microbial diversity and the characterization of predominate fungi of Liuyang Douchi are few. In present study, the Illumina HiSeq sequencing was performed to reveal the fluctuation characteristics of microbial diversity during fermentation. Results showed that Staphylococcus (33.86%), Staphylococcaceae_unclassified (27.39%) and Pediococcus (8.80%) were the dominated bacteria, while Petromyces (74.57%), Rhizopus (10.93%) and Penicillium (2.68%) were the most predominant fungi during entire fermentation period. Intriguingly, Petromyces was negatively correlated with Alternaria, Saccharomyces and Saccharomycetales_unclassified. Further, four non-aflatoxigenic Aspergillus flavus strains were first identified and isolated from Liuyang Douchi according to phylogenetic and macroscopic characteristics. These four Aspergillus flavus displayed high cellulase and protease activities, but weak lipase activity. This study could contribute to the quality control of Liuyang Douchi by providing an overview of the microbial diversity.