Soy sauce is a traditional fermented seasoning with unique flavor in which microbes play a crucial role. However, the correlation between core microbiota and characteristic flavor metabolites as well as physicochemical properties is not clear. In this study, high-throughput sequencing showed that Weissella, Tetragenococcus, and Lactobacillus were the marker bacteria for the initial, mid, and late stages of fermentation, respectively, while Aspergillus was predominant throughout the process, Candida and Zygosaccharomyces appeared mainly at the late stage. Additionally, 7 organic acids, 17 amino acids, and 52 volatile flavors were identified, of them, 24 compounds were recognized as the characteristic flavors. The color change of soy sauce was consistent with the bacterial succession. Correlation analysis between microbiota, physicochemical properties, and characteristic flavors suggested that Tetragenococcus, Lactobacillus, and Zygosaccharomyces were the potential core functional genera that affect the environment and characteristic flavors. These findings provided valuable insights for process optimization for fermented-food production.