Provided is a hybrid multi-epitope bivalent nucleic acid vaccine for preventing H3, H9 subtype flu, which pertains to the biotechnology field. The invention uses the influenza virus main epitope gene as the base, the Kozac sequence as the adjuvant gene, eukaryon expression vector pIRESlneo as the vector molecule, conducts artificial molecular design on the epitope gene under the computer aided simulation to obtain a safe and effective hybrid multi-epitope DNA vaccine aiming to a variety of serotypes and epidemic strains. The obtained nucleic acid vaccine can stimulate mouse to generate specific humoral immunity and cellular immunity, and the obtained vaccine is safe to the experimental animals, no pathological phenomenon are caused.