The invention relates to the technical field of polypeptide vaccines, and concretely relates to a screening and assessing method for a polypeptide vaccine. The method comprises the following steps: selecting a sequence with the pathogen neutralizing antigen epitope polypeptide sequence used as a polypeptide vaccine; carrying out a chemical process on the selected neutralizing antigen epitope to synthesize the polypeptide, and blocking active groups; coupling the polypeptide with a coupling carrier, eluting the uncoupled polypeptide, blocking the uncoupled coupling carrier, and cleaning the polypeptide-coupled coupling carrier for later use; filling a protein purifying column with the polypeptide-coupled coupling carrier, adding an antibody sample, and eluting and collecting a neutralizing antibody; and analyzing the neutralization titer of the captured neutralizing antibody through an in-vitro micro-neutralization test process. The invention also relates to an antigen epitope peptide having a neutralizing effect confirmed in early animal test, and the screening and assessing method for assessing whether the antigen epitope peptide is suitable for the human polypeptide vaccine or not. The screening and assessing method greatly improves the research and development efficiency of the polypeptide vaccine and reduces the research and development cost.