H7N9 avian influenza vaccines induce high levels of non-neutralizing (nonNeu) antibodies against the haemagglutinin (HA). However, the antigenic epitopes underlying this particular antibody response are still undefined. In this study, a panel of 15 monoclonal antibodies (mAbs) against the HA protein of H7N9 virus was generated and 14 of them had no hemagglutination inhibition and virus neutralizing activities. Four antigenic epitopes, including one linear and three conformational epitopes, in HA were identified using peptide-based enzyme-linked immunosorbent assay and biopanning of phage display random peptide library. More importantly, two mAbs (4B7 4D5 and 1B10 1D1) strongly inhibited HA-binding of chicken nonNeu antisera against viral-vectored H7N9 vaccine, whereas lower inhibition was observed for chicken neutralizing antisera. In contrast, there was weak competition between the mAb and murine nonNeu antisera against inactivated H7N9 antigen. The epitopes targeted by these two mAbs were defined as the immunodominant epitopes underpinning the elicitation of nonNeu antibodies by viral-vectored H7N9 vaccine. Additionally, the identified stalk epitopes were conserved among the H1-H17 subtypes and the stalk-reactive mAbs exhibited cross-reactivity with different subtypes. In conclusion, four novel nonNeu epitopes in H7N9 HA were identified, and two dominant epitopes underlying the induction of nonNeu antibodies by viral-vectored H7N9 vaccine were identified. Our results add new knowledge to the molecular basis for antibody immunity against H7N9 vaccines and provide useful implications for vaccine design and modification.