Natto, a nutritious fermented soybean product, is known for its health benefits. Modern production methods use Bacillus subtilis as the starter culture to ensure consistent quality. However, this method overlooks the potential positive effects of other microbial species present in traditionally, naturally fermented natto. This study explored the effects of ARTP-induced mutants of B. subtilis var. natto and several strains of lactic acid bacteria (LAB) on natto quality. The results showed that these two types of bacteria have complementary roles in fermentation. B. subtilis var. natto, with enhanced extracellular protease activity, promotes the hydrolysis of soy protein and enhances the product's ACE inhibitory and fibrinolytic activities. Meanwhile, two strains of Lactiplantibacillus plantarum reduced the content of total volatile basic nitrogen (TVB-N) while increasing the content of folic acid in the final product. In addition, B. subtilis var. natto and LAB produce different profiles of volatile compounds (VOCs). Subsequently, B. subtilis var. natto and Lpb. plantarum were used to co-ferment natto in different ratios. The results showed that the two types of bacteria could co-colonize and enhance fermentation quality through their respective strengths. Specifically, Lpb. plantarum strains co-metabolized with B. subtilis var. natto to elevate the content of pyrazines, characteristic VOCs in natto. The optimal quality of natto was achieved when Lpb. plantarum HIS6, Lpb. plantarum LP3 and B. subtilis var. natto Y15-11 were combined in a 2:1:2 ratio. This study not only identified effective combinations of starter cultures with complementary benefits but also elucidated the metabolic pathways of key volatile compounds. Our findings also provide technical insights for improving natto quality, enhancing consumer acceptance, and supporting industrial production.