The present invention provides hydrophobic heparin conjugates that are soluble in organic solvents but not in water, a method of preparing them, and a method of using them. Particularly, the present invention provides hydrophobic heparin conjugates that are prepared by covalently binding a polymer to heparin and a hydrophobic agent to the polymer. The hydrophobic heparin conjugates of the present invention maintain a good antithrombogenic effect and are insoluble in water due to their hydrophobicity, so they can be effectively used as coating agents for modifying the surfaces of medical devices.