The invention discloses a polypeptide vaccine against tumor-targeted drug resistance sites and a design method thereof. The design method includes the steps: collecting data of targeted drug resistance mutations; intercepting a drug resistance mutant polypeptide sequence and predicting the affinity and immunogenicity of MHC molecules; obtaining the relationship between targeted drugs and drug resistance sites, and performing drug clustering; and artificially designing a corresponding vaccine polypeptide sequence. The targeted drug combination polypeptide vaccine combination obtained by the method can cover common targeted therapeutic drugs, can effectively reduce the probability of tumor drug resistance, can prolong the effective action time of the targeted drugs, can increase the diseaseresponse rate of the patient, has broad-spectrum, can shorten the time from analysis to treatment of individualized peptide vaccines, and can reduce medical costs.