The present invention relates to sequences and structures of a class of polypeptides specifically binding with Japanese encephalitis virus envelope protein, and an application of the polypeptides in the anti-Japanese encephalitis virus drug targeting modification technology, and belongs to the technical field of biomedicine. According to the present invention, a phage display technology is adopted to screen a random peptide library to obtain the polypeptide having the sequence of number 1-11 and specifically binding with the envelope protein, the envelope protein binding peptide screened from the phage peptide library is subjected to researches such as binding activity with Japanese encephalitis virus and brain tissue targeting property, and results show that the polypeptide P63 having good specific binding activity with Japanese encephalitis virus and Japanese encephalitis virus infection mediated brain tissue targeting property is found, and the sequence is NH2-HHWWVPSWSRWT-COOH, such that the envelope protein binding peptide and the virus-specific brain-targeting peptide P63 are expected to be used in the targeting modification technology of the anti-Japanese encephalitis virus drugs.