QM/MM calculations have been used to elucidate the reaction mechanism of the reduction of acetylene to ethylene catalyzed by a nitrogenase-like enzyme DCCP_Ch with an unusual [Fe₈S₉] double-cubane cluster. Various plausible reaction pathways, involving different oxidation states and protonation states of the iron-sulfur cluster, have been analyzed to find the most favorable one. The acetylene substrate bridges to the [Fe₈S₈] cluster via its triple bond in a μ-(bis-η²) coordination mode. After a proton-coupled electron transfer reduction of the reactant complex, the acetylene reduction may be described to proceed via a special “double-electron transfer induced proton transfer” mechanism, deduced from the principal interacting orbital analysis. The anti-ferromagnetically coupled [Fe₈S₈] cluster delivers a pair of α- and β-electrons to the substrate, concertedly but asynchronously with a proton transfer mediated by the second-shell Lys147 residue to one of the acetylene carbon atoms. Subsequently, the second proton-coupled electron transfer proceeds, followed by protonation of the substrate to afford the ethylene product. During the two-electron reaction, the oxidation states of the [Fe₈S₈] cluster cycle from [Fe^II₆Fe^III₂], to [Fe^II₇Fe^III], to [Fe^II₅Fe^III₃], and back to [Fe^II₆Fe^III₂].