Middle East Respiratory Syndrome coronavirus (MERS-CoV) was first identified in 2012, which led to 704 deaths with a mortality rate of ~34.7% up till June 2017. Nevertheless, there is no approved antiviral medicines or standard guideline for treating MERS-CoV infected patients. MERS-CoV encoded proteins such as M protein, ORF4a, ORF4b, and ORF5, were found to have interferon (IFN) antagonizing properties, which correlates with the reduced IFN expression in different experimental models. In this study, we demonstrated the therapeutic potential of type I interferon during MERS-CoV infection with an ex vivo human respiratory tract explants cultures; a cyclophilin inhibitor was also used in addition to type I interferon as the reagent of combination therapy. Briefly, human lung and bronchus tissues were obtained from patients who underwent surgical resection in Queen Mary Hospital, Hong Kong SAR. Ex vivo infection was performed on explants culture of human lung and bronchus with HCoV-EMC. Post-infection administration regimes of type I interferon and/or cyclophilin inhibitor were applied. Supernatants of the infected culture were collected at 1, 8, 24, 40, 56 hpi, and virus replication kinetics were determined by TCID50 assay. The results showed that both type I Interferon and cyclophilin inhibitor significantly inhibit MERS-CoV replication. The effect of inhibition was most significant with the using of both type I interferon and cyclophilin inhibitor, which also induced higher level of ISGs expressions. In summary, our study demonstrated that the combined treatment of type I interferon with cyclophilin inhibitor is potent for inhibiting MERS-CoV replication in ex vivo human bronchus explants culture. This novel potential therapy for severe human coronavirus infection warrants rapid clinical investigation.