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This invention relates to a recombinant hirudin fusion protein with collagen affinity, its preparation method, and its applications. The fusion protein is a recombinant hirudin fusion protein incorporating a collagen-binding domain (CBD). The fusion protein of this invention possesses affinity for type I and type III collagen, and can inhibit thrombin activity to exert an anticoagulant effect. Furthermore, it can bind well to collagen-based composite materials, making it suitable for use in cardiovascular implants such as heart valves, cardiac occluders, dialysis membranes, oxygenation membranes, artificial blood vessels, and vascular stents, as well as in extracorporeal circulation and blood purification devices, enhancing anticoagulant and antithrombotic effects.