Understanding the influences of electrode characteristics on charge transport is essential in the field of molecular electronics. In this study, we investigated the electronic transport properties of molecular junctions comprising methylthiol-terminated permethyloligosilanes and face-centered crystal Au/Ag electrodes with crystallographic orientations of (111) and (100), based on ab initio quantum transport simulations. The calculations revealed that molecular junction conductance was dominated by the electronic coupling between two interfacial metal–S bonding states, which can be tuned by varying the molecular length, metal material of the electrodes, and crystallographic orientation. As the permethyloligosilane backbone elongated, although the σ conjugation increased, the decreasing coupling induced by the increasing number of central Si atoms reduced the junction conductance. The molecular junction conductance of methylthiol-terminated permethyloligosilanes with Au electrodes was higher than the molecular conductance of those with Ag electrodes with a crystallographic orientation of (111). However, the conductance trend was reversed when the electrode crystallographic orientation was varied from (111) to (100), which can be ascribed to the reversal of interfacial coupling between two metal-S interfacial states. These findings can help elucidate the mechanism of molecular junctions and improve the transport properties of molecular devices by adjusting the electrode characteristics.