As a typical representative of Chinese rice wine (Huangjiu), Hongqu rice wine is famous for its red color, mellow taste and strong fragrance. However, due to the open brewing environment and traditional fermentation technology, there are some safety risks in traditional brewed Hongqu rice wine, such as a certain amount of biogenic amines. In this study, the dynamic changes and the differences of microbial communities and volatile flavor components between two types of Hongqu rice wine with high and low biogenic amine contents (LBAW and HBAW) during the traditional brewing were systematically investigated. The results showed that the total biogenic amine contents in LBAW and HBAW were 20.91 and 69.06 mg/L, respectively. The contents of putrescine, cadaverine, spermine and spermidine in HBAW were significantly higher than those in LBAW, and it was noteworthy that spermine content in HBAW was 17.62 mg/L, which was not detected in LBAW. In addition, the volatile flavor characteristics of the two kinds of Hongqu rice wine were obviously different. The contents of acetophenone, n-butyl butanoate and benzothiazole were obviously higher in HBAW, while the contents of isoamyl acetate, ethyl lactate, ethyl caprate and phenylethyl alcohol were significantly higher in LBAW. High-throughput sequencing of 16S/ITS amplicon revealed that Weissella, Kosakonia, Pantoea, Monascus, Saccharomyces and Millerozyma were the predominant microbial genera during the traditional brewing of HBAW, while Weissella, Kosakonia, Monascus, Saccharomyces and Issatchenkia were the predominant microbial genera during the traditional brewing of LBAW. Correlation analysis revealed that biogenic amines were significantly negatively correlated with unclassified_o_Saccharomycetales, Cyberlindnera, Zygoascus, Aspergillus and Acinetobacter, but positively correlated with Lactobacillus, Pediococcus, Millerozyma and Apiotrichum. In addition, we also found that Lactobacillus, Pediococcus and Saccharomyces were significantly positively correlated with most of the volatile flavor components, while Candida, Trichosporon and Monascus were significantly negatively correlated with most of the volatile flavor components. In addition, bioinformatical analysis based on PICRUSt demonstrated that the key enzymes for biogenic amine biosynthesis were more abundant in the microbial community of HBAW than LBAW. These findings demonstrate that the formations of volatile flavor and biogenic amines in Hongqu rice wine are influenced by microbial community during the fermentation. This work facilitates scientific understanding of the formation mechanism of biogenic amines, and may be useful to develop effective strategies to improve the quality of Hongqu rice wine.