Hirudin is one of the most potent anti-coagulant protein ever found, and its C-terminus is a key domain for inhibiting thrombin. In order to enhance its specificity, a novel anti-coagulant protein was constructed via fusing the C-terminus of hirudin to AnnexinⅤ, which was expected to sustain both anti-coagulant activity and phorspholipid affinity. The structure of the designed protein was predicted with both molecular mechanics and dynamics. Molecular dynamics was adopted to simulate the docking interaction between the fusion protein and thrombin. The results showed the inhibitory activity of the fusion protein to thrombin.