The invention discloses an anticoagulation high polymer biomaterial which comprises a substrate layer, an anticoagulation coating, and a plasma polymerization layer positioned between the substrate layer and the anticoagulation coating, wherein the substrate layer is made of a biomedical material; the plasma polymerization layer is an allylamine plasma polymerization membrane layer deposited on the substrate layer; the anticoagulation coating is an anticoagulant layer fixed on the plasma polymerization layer; and the anticoagulants comprise hirudin, heparin and the like. Anticoagulant molecules are fixedly grafted on the material surface by utilizing the pulsed plasma technology and surface heparin grafting method, and effective molecule orientation is remained by heparin molecules, so the anticoagulant performance is close to the performance of heparin molecules in the solution. Meanwhile, the heparin molecules are difficultly scoured off by blood, the persistence and stability of the anticoagulation effect are guaranteed, and the service life is long. The invention further discloses a preparation method and application of the anticoagulation high polymer biomaterial.