Abstract: To study the effect of fortified Zygosaccharomyces rouxii (JL-02) on the quality of soy sauce, salt tolerance characteristic of strain JL-02, pH and neutral proteinase activity of koji, the physicochemical properties and volatile flavor substances of two soy sauces in different brewing processes were analyzed. The results showed that salt tolerance of the strain JL-02 was up to 16%, the pH of koji was 6.85±0.08, and the neutral proteinase activity reached to (2109.2±45.2) U/g. Compared with the control group, the soy sauce treated with fortified Zygosaccharomyces rouxii exhibited the increased total acid content ((1.14±0.01) g/100 mL), decreased reducing sugar content ((1.06±0.01) g/100 mL) and pH value (5.09±0.03). But there was no significant difference in the content of amino nitrogen, and all samples reached the standard of special grade soy sauce. In addition, there were 15, 52 and 57 volatile flavor compounds in the koji, control group, and experimental group, respectively. And the furan flavor substances (2-pentylfuran, 4-methoxy-2,5-dimethyl-3(2H)-furanone and 2,3-dihydrobenzofuran) were increased in the experimental group. The principal component analysis of the volatile flavor compounds in the three groups of samples showed a good result. This research provides a theoretical basis and technical reference for the soy sauce enterprises to carry out the intensified yeast strain brewing soy sauce technology in the future.