The invention discloses a fusion protein for resisting formation of thrombus targetedly, which comprises the following parts: (a) protein domains of nematode anticoagulant peptide 5, of which the amino acid sequence has at least 80 percent of similarity with a sequence shown as SEQ ID No.1; (b)protein domains of Hirulog, of which the amino acid sequence has at least 80 percent of similarity with a sequence shown as SEQ ID No.2; (c) protein domains of RGD peptide, consisting of 3 to 10 amino acids and containing an Arg-Gly-Asp sequence; and (d) human coagulation factor X a recognition sites, of which the amino acid sequence is shown as SEQ ID No.3. The invention also discloses a gene encoding the fusion protein, a recombined expression vector containing the gene, a transformant containing the recombined expression vector, and a method for preparing the fusion protein. The prepared fusion protein can inhibit formation and development of thrombus from a plurality of approaches and take effect on thrombus positions targetedly, and is suitable for preventing and treating thrombotic disorders.