The invention discloses a method for improving the flavor of bacillus natto fermented whole-soybean milk, and belongs to the technical field of fermented soybean product processing. With soybeans being raw materials, whole-soybean milk is prepared through the technology of selecting, soaking, hot water heating, coarse smashing, ultrafine smashing and high-pressure homogenizing, bacillus natto and lactic acid bacteria are separately inoculated into the sterilized and cooled whole-soybean milk to be fermented, then bacillus natto fermented soybean milk and lactic acid bacterium fermented soybean milk are mixed and blended according to a proportion, and then the whole-soybean milk is obtained. While the taste is guaranteed, the soybeans are fully utilized, in this way, pollution to the environment is avoided, and the capacity, for generating acid and aroma in the soybean milk, of lactic acid bacteria is utilized for effectively improving the flavor of the fermented soybean milk. Meanwhile, the liquid fermentation technology that bacillus natto and lactic acid bacteria are separately fermented and then blended is adopted, pipeline transportation can be achieved, control over fermentation conditions and a fermentation end point is easier, the range is easy to enlarge, the components are easy to control, and follow-up processing is simple.