The invention discloses a biological antibacterial polypeptide preparation as well as a preparation method and application of the biological antibacterial polypeptide preparation. The biological antibacterial polypeptide preparation takes water as a carrier and is prepared from the following components in percentage by weight: 0.1 percent to 10 percent of a biological antibacterial peptide BQ and 0.01 percent to 1 percent of polyhexamethylene biguanidine. The biological antibacterial polypeptide preparation has good sterilization effect. A core sterilization component of the preparation is a novel antibacterial peptide and has very high sterilization effect on staphylococcus aureus, escherichia coli, candida albicans and viruses. When an in-vitro experiment is carried out for 2min to 5min, 99.9 percent of sterilization rate can be realized. The biological antibacterial polypeptide preparation has high safety, has no toxicity to or residues to human bodies, has high stability and can be used as a prevention medicine. The main acting component is a biological preparation and the disadvantages that a traditional chemical preparation has irritation on mucosa and bacteria easily have drug resistance are overcome. The biological antibacterial polypeptide preparation is easily accepted by organisms, has no toxic side effect and is suitable for long-time utilization or used as the prevention medicine.