Abstract: Soy sauce, as a traditional Chinese condiment, is well loved for its unique savory and delicious taste. The complex flavor quality in soy sauce is closely related to the metabolism of various microorganisms during the traditional brewing. In recent years, with the widespread application of high-throughput sequencing, macrogenomics and macrotranscriptomics, the diversity of microbial communities and their functions are a hot topic in soy sauce research. This paper reviews the research progress on the identification of microbial communities in soy sauce fermentation, the structural composition of soy sauce microbial communities, the core microbial differences and their succession patterns based on the spatial and temporal dimensions, and the core microbial strains and their functional roles, and introduce the current status of soy sauce microbial community research under the traditional culture and non-culture techniques. The diversity of prokaryotic and eukaryotic microorganisms during the fermentation of different soy sauce processes in China, especially the roles and patterns of change of the core microorganisms in soy sauce, such as Aspergillus oryzae, Tetrahymena salinophila, Weissella, Zygosaccharomyces rouxii, and Candida, as well as the driving factors. The core microorganisms have different functional roles in the soy sauce fermentation process. On this basis, the research on microbial communities in soy sauce is prospective, and it is suggested that emerging technologies such as multi-omics, artificial intelligence, and machine learning should be applied in the future to further reveal the relationship between microbial community interactions and the formation of distinctive flavors, with the aim of providing a scientific basis and prospective suggestions for the application of microbial community regulation technology and synthetic microbial community technology in the soy sauce industry.