The invention discloses a preparation method of a hydrolyzed whey protein cross-linked product, and belongs to the technical field of cross-linked protein preparation, and the method comprises the following steps: carrying out enzymolysis on whey protein isolate by utilizing trypsin to obtain a whey protein isolate hydrolysate. And carrying out cross-linking on the hydrolysate by using glutamine transaminase to obtain the hydrolyzed whey protein isolate cross-linked substance. Specifically, enzyme hydrolysis and glutamine transaminase cross-linking are combined to modify the whey protein, the thermal stability of the whey protein with high thermal stability is obtained, and cross-linking after hydrolysis can further increase the apparent viscosity of the whey protein at the same time. According to the invention, the whey protein is treated by using a method of combining enzyme hydrolysis and enzyme crosslinking, the influence of change factors in two modification processes on the structure and functional characteristics of a final product is analyzed, and the hydrolyzed whey protein cross-linked product with good thermal stability and high apparent viscosity is obtained, thereby providing a theoretical basis and technical support for modifying the whey protein. The wide application of the whey protein is promoted.