We investigated the change in the metal–molecule interaction in a 1,4-benzenedithiol (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.