The understanding of the interfacial effect on charge transport is essential in single-molecule electronics. In this study, we elucidated the transport properties of molecular junctions comprising thiol-terminated oligosilane with three to eight Si atoms and two types of Ag/Au electrode materials employing different interfacial configurations. First-principles quantum transport calculations demonstrated that the interfacial configuration determines the relative magnitude of the current between the Ag and Au electrodes, wherein the Ag monoatomic contact configuration presented a larger current than did the Au double-atom configuration. Further, the mechanism of electron tunneling from the interfacial states through the central σ channel was revealed. In contrast to Au double-atom electrodes, Ag monoatomic electrodes exhibit a higher current due to the presence of Ag–S interfacial states closer to the Fermi level. Our findings show that the interfacial configuration is a plausible way to generate the relative magnitude of current of thiol-terminated oligosilane molecular junctions with Au/Ag electrodes and provide further insight into the interfacial effect on the transport properties.