The invention discloses a fusion protein with antibacterial function and an application thereof. The gene sequence compositions of the fusion protein are hepcidinl precursor antibacterial peptide gene which is obtained by cloning and synthetic magainin antibacterial peptide which are combined as a novel fusion protein cDNA and integrated into a yeast gene group by the gene engineering means; the fusion protein cDNA is induced to express at the yeast, and furthermore, the yeast ferments and cultivates to obtain a plurality of fusion protein. The fusion protein of the invention is detected having obvious antibacterial activity, is applied to prevent and remedy the bacterial disease of aquatic organisms and cultured animals, or the purified fusion protein is directly used as a drug to replace antibiotic to be applied to the treatment of the disease caused by bacteria and even virus.