The formation of methyl-Ni(F-430) species in methyl-coenzyme M reductase (MCR) has been investigated using the B3LYP hybrid density functional method and an active-site model built on the basis of X-ray crystal structure. CH3-I, CH3-Br, CH3-Cl, and CH3-S-CH3 were chosen as the substrates, the last one regarded as a model of the native substrate (methyl-coenzyme M, CH3-SCoM). The calculations indicate that the formation of CH3-Ni(F-430) in MCR is dependent on the acidity of the substrate leaving group. A CH3-Ni(F-430) species has been observed with methyl halides as substrates, while the formation of CH3-Ni(F-430) from the native substrate is demonstrated to be inaccessible energetically. These results agree well with the current experiments.