This study aimed to obtain strains producing high levels of salt-tolerant protease from Aspergillus oryzae K9, isolated from high-salt liquid-state moromi, by combined mutagenesis induced by atmospheric and room temperature plasma (ARTP) and ultraviolet (UV) followed by domestication and screening using high-salt plates. The dominant mutant S-G27, whose neutral protease activity was increased by 35.82% compared with K9, was obtained after ARTP treatment of K9. The dominant mutant G-U2, whose neutral protease activity was increased by 56.81% compared with K9, was obtained after subsequent UV treatment of S-G27. In 15% NaCl solution, the residual activity of neutral protease from G-U2 was 1.94 times as high as that of K9. G-U2 exhibited good stability, and 92% of the initial enzyme activity remained after the seventh passage. Compared with the starting strain K9, G-U2 showed shorter mycelia, more spores, larger spore volume, and more surface ornaments. Mutagenesis did not induce the expression of aflatoxin-related genes, meeting production safety requirements. In simulated soy sauce fermentation experiments, the neutral protease activity, acid protease activity, and amino nitrogen content of G-U2 at the end of fermentation were 120.19%, 52.29%, and 18.37% higher than those of K9, respectively.