Summary Zygosaccharomyces rouxii and Candida versatilis are important flavour‐producing yeasts in soy sauce fermentation. In the present study, the interaction between Z. rouxii and C. versatilis co‐cultures in YPD and raw soy sauce medium was investigated and applied to soy sauce fermentation. The concentration of Z. rouxii in the co‐culture was 0.47 times that in the mono‐culture. This observation suggested that C. versatilis inhibited the growth of Z. rouxii, likely attributed to various factors, including the production of acids and heat‐ and protease‐sensitive substances by C. versatilis . Furthermore, we examined the physicochemical properties and characteristic volatile flavour components of soy sauce by adding varying ratios of Z. rouxii and C. versatilis at different stages of fermentation. The results showed that mixed fermentation of Z. rouxii and C. versatilis enhanced the total nitrogen, amino acid nitrogen, 4‐hydroxy‐2(5)‐ethyl‐5(2)‐methyl‐3(2H)‐furanone, and volatile compounds in soy sauce compared to single‐strain fermentation. Additionally, optimal soy sauce results were obtained when yeasts were added on day 45, with an inoculation ratio of 1:1. In conclusion, during the moromi fermentation stage, the appropriate selection of the inoculation ratio and time for Z. rouxii and C. versatilis addition can effectively enhance the physicochemical properties and flavour attributes of soy sauce.