High magnetic property chitosan particles were prepared from chitosan coated on magnetic powder, glutaraldehyde modified, and then epichlorohydrin crosslinked. The magnetic properties, the surface, and the morphology of the magnetic particles were characterized. An optimum condition of immobilization of aprotinin on magnetic particles was obtained, then these particles were used for affinity purification of trypsin, and the condition of affinity purification was discussed. The proposed method was successfully applied to the purification of trypsin.