Microbial populations in the brewing of soy sauce are abundant， diverse and complex. The aim of this study was to gain a better understanding of global microbial diversity during the soy sauce fermentation process. Succession and spatial heterogeneity of microbial community in soy sauce production were analyzed by high-throughput sequencing at the stages of koji-making， mash fermentation and sauce extraction. The results showed that the microbiota diversity， community composition， and functional properties of microbial community in soy sauce fermentation exhibited distinct stages and spatial heterogeneity. In the analysis of alpha and beta diversity， the bacteria diversity were higher than that of fungi. The microbiota exhibited a higher biodiversity in the stages of mash fermentation and sauce extraction than in the koji-making. The mash from the upper layer exhibited high bacterial diversity and the lower layer exhibited high fungal diversity. In the analysis of community composition， there were 147 bacterial genera and 19 fungal genera by amplicon sequencing during the soy sauce production. Staphylococcus， Weissella， and Tetragenococcus were the core bacterial genera. Aspergillus and Zygosaccharomyces were the core fungal genera. Each microorganism showed abundance differences in time and space. In the analysis of functional predication， the major bacterial function was amino acid metabolism， and the major fungal functions were carbohydrate and fat metabolism. Conclusively， this study revealed the effects of fermentation time and space on microbial community during the fermentation process of soy sauce， and provided basic data for the further study of microbiome quality control， regulation of community composition， and optimization of process conditions in soy sauce brewing.