Disclosed herein is a method of preparing an antithrombotic agent from muskrat musk and an antithrombotic agent having a high potency obtained therefrom, wherein the antithrombotic agent is prepared by treating muskrat musk with ethanol to obtain an ethanol extract; carrying out two normal phase column chromatographies while raising the combination ratio of hexane and ethyl acetate to obtain numerous fractions; carrying out thin layer chromatographies and identifying the material patterns of the fractions with UV lamps and 10% sulfuric acid to divide the materials which have a similar moving distance into groups; measuring a thrombin time of each group to isolate a group having a potent antithrombotic activity; carrying out a reverse phase column chromatography while raising the combination ratio of acetonitrile and water to obtain numerous fractions; and isolating an antithrombotic agent material having a high potency therefrom. According to the present invention which provides an antithrombotic agent having a high potency from muskrat musk, the value added of muskrat musk is raised.