To investigate the abundance and function of Tetragenococcus halophilus in the Japanese style soy sauce fermentation process, this study first quantified its absolute abundance in soy sauce moromi samples at different fermentation stages using chip-based digital PCR(dPCR). Subsequently, nine T. halophilus strains were isolated from the soy sauce moromi, and their growth curves under different mass fraction of NaCl and pH conditions were plotted. The strain YC24, which exhibited the best growth performance, was selected for whole-genome sequencing, metabolic function annotation, and analysis of genes related to salt stress response, while the auxiliary metabolic functions of its prophage were also explored. The results showed that the absolute abundance of T. halophilus increased initially and then declined, reaching a peak of 1.86×106 copies/g on the 60th day of fermentation. The optimal growth conditions for T. halophilus were found to be 10%(mass fraction) NaCl and pH 7.0. The genome size of strain YC24 was 2 328 497 bp, with a G+C content of 35.69%, and a total of 2 232 COG functional genes, 1 065 KEGG functional genes, and 227 carbohydrate-active enzymes were annotated. Additionally, YC24 was found to carry multiple genes associated with the synthesis and transport of osmoprotectants, and one prophage was identified, in which two auxiliary metabolic genes were annotated. In conclusion, T. halophilus exhibited significant ecological adaptability and functional potential in soy sauce fermentation through its participation in various metabolic pathways.