A method of processing low-value fish antibacterial peptides is disclosed. The method includes steps of preparing, sterilizing, degreasing, performing microwave extraction for purification, performing centrifugal purification, performing enzymatic hydrolysis, performing centrifugal purification, and performing purification with ammonium sulfate to obtain a finished product. Swim bladders of low-value fish are degreased, impurities are removed by filtration, proteins in the swim bladders are purified, then the enzymatic hydrolysis is performed to hydrolyze the proteins into antibacterial peptides, and enzymatic-activity peptides are used to increase activity of compound protease, thus accelerating hydrolysis and increasing the processing efficiency. Beneficial effects of the method are that the swim bladders of low-value fish are utilized to produce the antibacterial peptides to achieve high-value utilization of the swim bladders, the antibacterial peptides prepared by the method have characteristics of capability of being natural, nontoxic, pollution-free, antibacterial, efficient, wide in antibacterial spectrum, and the like, and the finally obtained antibacterial peptides are high in yield and purity, can be applied in industrial production and have a good development prospect.