The Middle East respiratory syndrome coronavirus (MERS-CoV) has caused outbreaks of a SARS-like illness with high case fatality rate since 2012.The reports of its personto-person transmission through close contacts have raised a global concern about its pandemic potential.The spike protein S2 of MERS-CoV mediated the fusion process between the viral membrane and target cell membrane.The fusion core of S2 protein serves as the ideal target for developing MERS-Cov fusion inhibitors, like T20 (enfuvirtide) for HIV infection.Here we solved the crystal structure of the six-helix bundle fusion core of S2 protein.Based on this novel structure, we designed several candidate inhibitory peptides.Then we found a HR2P peptide could potently inhibit the MERS-Coy infection and the S2 fusion core formation.Moreover, the introduction of hydrophilic residues into HR2P could further improve the stability, solubility and antiviral activity of HR2P inhibitor.Therefore, the HR2P analogues have good potential to be further developed into effective viral fusion inhibitors for treating MERS-CoV infection.