In the present study, we designed a novel targeted multi-functional fusion protein LHAD composed of LL-37, FXa recognition peptide, hirudin-12-residue, AAP, and RGD peptide. It was expressed in the Pichia pastoris GS115 strain and purified by affinity chromatography. The in vitro studies suggested that the novel designed protein exhibited antibacterial activity, anti-platelet aggregation and anti-thrombin activities. Moreover, the capability of anti-thrombin was significantly increased compared to that of natural hirudin. Our study may provide a potential approach to design multi-functional drugs for the prevention and management of thrombosis.