Abstract: In order to address the problems of solid-state fermentation of nattokinase, such as uncontrollable conditions, low enzyme production, and poor flavor, this paper carried out a study from the optimization of culture medium, compounding of grains and fermentation at different temperatures. Firstly, the solid-state fermentation medium and fermentation conditions were optimized by single-factor and response surface, secondly, the enzyme yield and flavor were further improved by soybean crushing, grain compounding, and temperature-change fermentation. Then, the samples were analyzed for volatile flavor substances and volatile saline nitrogen, and lastly, the isoflavones content was determined by high-performance liquid chromatography (HPLC) and analyzed for antioxidant activity. The results showed that when using soybeans as the raw material, with an inoculum amount of 5.8%, sucrose at 2.18%, tryptone at 1.51%, KCl at 0.1%, and fermentation at 30 °C for 24 h, the nattokinase activity was 9924.81 IU/g, and the enzyme production increased by 81.87%. When soybeans were split into halves and compounded at a soybean-to-soybean meal mass ratio of 4:1, fermentation at 30 °C for 24 h followed by transfer to 40 °C for 8 h resulted in an enzyme activity of 18453.77 IU/g, representing a 238.17% increase over pure soybean fermentation. Compounding with grains weakened the off-flavor and reduced volatile basic nitrogen by 17.22%. Meanwhile, the fermented samples with grain compounding showed increased active components, with soybean isoflavones and total antioxidant capacity rising by 39.95% and 20.60%, respectively. This study demonstrates that effective improvement of nattokinase yield and active components, along with reduction of fermentation-derived peculiar smells, can be achieved through adjusted raw material pretreatment and optimized fermentation conditions, providing a theoretical basis and technical support for efficient nattokinase production.