Belonging to the field of agricultural product processing and by-product comprehensive utilization, the invention relates to a method for recovery of Kunitz and Bowman-Birk trypsin inhibitors from soybean whey. The method of the invention comprises the steps of: (1) pretreatment of soybean whey; (2) primary separation of whey soy protein; (3) complex coacervation of soybean whey protein and polyanionic polysaccharide; and (4) recovery of Kunitz and Bowman-Birk trypsin inhibitors. By subjecting the raw material to pretreatment, primary separation and complex coacervation, a final protein polysaccharide compound can be obtained, and after ultrafiltration for sugar removal, ultrafiltration for desalination, and twice centrifugation on the final protein polysaccharide compound, a protein solution containing purified Kunitz and Bowman-Birk trypsin inhibitors can be obtained, and through vacuum freeze drying of the protein solution, Kunitz and Bowman-Birk trypsin inhibitor high purity samples can be obtained. The method provided by the invention has the characteristics of comprehensive utilization of soybean whey, low equipment requirement, simple operation, and no environmental pollution. And the trypsin inhibitors have high recovery rate, high purity, and high protein activity.