Electron transport through noncovalent interaction is of fundamental and practical importance in nanomaterials and nanodevices. Recent single-molecule studies employing singlemolecule junctions have revealed unique electron transport properties through noncovalent interactions, especially those through a π−π interaction. However, the relationship between the junction structure and electron transport remains elusive due to the insufficient knowledge of geometric structures. In this article, we employ surface-enhanced Raman scattering (SERS) synchronized with current−voltage (I−V) measurements to characterize the junction structure, together with the transport properties, of a single dimer and monomer junction of naphthalenethiol, the former of which was formed by the intermolecular π−π interaction. The correlation analysis of the vibrational energy and electrical conductance enables identifying the intermolecular and molecule−electrode interactions in these molecular junctions and, consequently, addressing the transport properties exclusively associated with the π−π interaction. In addition, the analysis achieved discrimination of the interaction between the NT molecule and the Au electrode of the junction, i.e., Au−π interactions through-π coupling and though-space coupling. The power density spectra support the noncovalent character at the interfaces in the molecular junctions. These results demonstrate that the simultaneous SERS and I−V technique provides a unique means for the structural and electrical investigation of noncovalent interactions.