High salt conditions negatively affect the fermentation efficiency of soy sauce and human health. This study aimed to construct a synthetic microbial community based on dominant functional microorganisms for salt-reduced soy sauce fermentation by investigating the succession and function of the microbial community during factory soy sauce fermentation. The findings revealed that the interplay between salinity and microorganisms influenced the dynamic changes of microbial communities. Furthermore, Aspergillus, Wickerhamomyces, Zygosaccharomyces, Staphylococcus, Weissella, and Tetragenococcus were analyzed to play key roles during soy sauce fermentation. Subsequently, the core strains were isolated and their strains and metabolic characteristics were evaluated. Finally, six strains (Aspergillus oryzae JQ09, Wickerhamomyces anomalus HJ07, Zygosaccharomyces rouxii JZ11, Staphylococcus carnosus QJ26, Weissella paramesenteroides ZJ19, and Tetragenococcus halophilus GY03) were employed to reconstruct the synthetic microbial community and conduct salt-reduced soy sauce fermentation. Biofortification increased the accumulation of metabolites in salt-reduced soy sauce. When the salt content was reduced to 14%, the sensory characteristics of soy sauce were closest to those of traditional soy sauce. Overall, this research presents a bottom-up approach to establish a simplified microbial community model with desired functions through deconstructing and reconstructing microbial structure and function. It has the potential to enhance the fermentation efficiency and realize the fermentation of salt-reduced traditional fermented food.