The invention discloses a preparation method of chitosan/silk fibroin microspheres for thrombin immobilization. The method comprises steps as follows: S1, degummed fibroin fiber is added to an ethanol solution containing calcium chloride to be dissolved, and a fibroin solution is obtained after dialysis and filtration; S2, chitosan is dissolved in an acetic acid solution, the fibroin solution in S1 and a CuSO4 solution are added, and a mixed solution is obtained; S3, the mixed solution in S2 is added to an alkaline ethanol solution, hollow beads are prepared, EDTA is added, complex Cu2<+> is removed through stirring, dehydration, cleaning and drying are performed after filtration, and chitosan/fibroin beads are obtained; S4, chitosan/fibroin beads in S3 are swelled, a thrombin solution and a buffer solution are added, and a glutaraldehyde solution is added for an immobilized enzyme reaction. Chitosan and fibroin are used as carriers for immobilized enzyme, the enzyme stability can be improved, the immobilization activity recovery efficiency is guaranteed, and the method has great actual significance.