We investigated the change in the metal−molecule interaction in a 1,4benzenedithiol (BDT) single-molecule junction using a combination of surface-enhanced Raman scattering spectra and current−voltage curves. During the stretching process, the conductance of the junction systematically decreased, accompanied by an increase in the vibrational energy of the CC stretching mode. By analyzing the current−voltage curves and Raman spectra, we found that the interaction between the π orbital of BDT and the electronic states of Au was diminished by the orientation change of BDT during the stretching process. A comparison with a 4,4′-bipyridine single-molecule junction revealed that the reduction of coupling of the Au−S contacts was smaller than that of Au−pyridine contacts. Therefore, the electronic states originating from the contact geometry are responsible for the tolerance to the stretching of thiol-terminated molecular junctions.