The invention provides a hybrid antimicrobial peptide FW-CP and a preparation method and an application thereof. The present invention is based on the spatial structure analysis of amino acid sequences of the chicken-derived antimicrobial peptide Fowlicidin-2 and the porcine-derived antimicrobial peptide cecropin P1, the antibacterial peptide Fowlicidin-2 is spliced with the antibacterial peptidececropin P1, the protein Lingker is added in the middle, amino acid mutation of the partial site is carried out to obtain the novel hybrid antimicrobial peptide FW-CP, and the antibacterial efficacy can be significantly improved. On the basis, a pichia yeast preferred codon is selected to artificially synthesize the novel hybrid antimicrobial peptide FW-CP gene which is cloned into pichia yeast toexpress to obtain a novel antibacterial peptide recombinant yeast strain, and the fermentation scale is amplified to the level of a fermentation tank, so that the high-density fermentation and efficient expression of an antibacterial peptide product are realized. After being further purified, a fermentation solution can be prepared into powder, liquid and other antibacterial peptide preparationsfor preventing and treating livestock and poultry diseases.