We have investigated the effect of the bias voltage on the 1,4-benzenethiol (BDT) single-molecule junction using the surface-enhanced Raman scattering (SERS). By measuring the bias voltage dependence of SERS for the identical sample, we can clearly observe the blue shift of the vibrational mode at 355 cm–1 by the application of the bias voltage. This measurement is possible by using a highly stable nanogap electrode which is fabricated with lithographic techniques. Meanwhile, the energy of other vibrational modes does not change with the bias voltage. The change in the bond strength can be explained by the charge transfer induced by the application of the bias voltage on the single-molecule junction. The theoretical calculation result reveals that the effect of bias voltage is a result of the rearrangement of the π system. The 355 cm–1 mode is an out-of-plane mode of the aromatic ring. In the BDT single-molecule junction, the π system is delocalized on the sulfur atom. This delocalization is suppressed by the application of the bias voltage, and thus, the aromatic ring is more “benzene-like” and the out-of-plain vibration shifts to higher energy.