Recombinant proteins bearing one (sM2) or three (3sM2) copies of M2 epitope from influenza virus were expressed in Escherichia coli. Mice were administrated with these two proteins and systemic and mucosal immune responses were analyzed. Compared with sM2, 3sM2 induced M2-specific serum IgG and mucosal IgA antibodies with neutralizing activity more efficiently in the whole immune course and the later mucosal immunization improved this advantage. MDCK cells pretreated with 3sM2 antisera showed less pathogenic morphological changes compared with that of pretreated with sM2. Together, our results demonstrated that high epitope density in one recombinant protein can enhance humoral immune responses in both systemic and mucosal immunization, and combination of systemic and mucosal immunization enhances this advantage.