Specifying the geometric and electronic structures of a metal–molecule interface at the single-molecule level is crucial for the improvement of organic electronics. A single-molecule junction (SMJ) can be used to investigate interfaces because it can be regarded as an elementary unit of the interface structure. Although considerable efforts have been made to this end, the detection of structural changes in SMJs associated with metal–molecule interactions remains challenging. In this study, we detected the surface-enhanced Raman scattering (SERS) signal originating from the metal–molecule interaction change induced by a local structural change in a C60 SMJ. This junction has attracted wide attention owing to its unique electronic and vibronic properties. We fabricated a C60 SMJ using a lithographically fabricated Au electrode and measured the SERS spectra along with the current–voltage (I–V) response. By continuous measurement of SERS for the C60 SMJ, we obtained SERS spectra dependent on the local structural change. The analysis of the I–V response revealed that the vibration energy shift originates from the change in the local structure for different Au–C60 interactions. Based on the discrimination of the states in accordance with the Au–C60 interaction, we found that the probability of SERS for geometry with a large Au–C60 interaction was enhanced.