Quantum tunneling plays an important role in coupled plasmonic nanocavities with ultrasmall gap distances. It can lead to intriguing applications such as plasmon mode excitation, hot carrier generation, and construction of ultracompact electro-optic devices. Molecular junctions bridging plasmonic nanocavities can provide a tunneling channel at moderate gap distances and therefore allow for the facile fabrication of quantum plasmonic devices. Herein we report on the large-scale bottom-up fabrication of molecular junction-bridged plasmonic nanocavities formed from Au nanoplate-Au nanosphere heterodimers. When the molecular junction turns from insulating to conductive, a distinct spectral change is observed, together with the emergence of a high-order charge transfer plasmon mode. The evolution of the electron tunneling-induced plasmon mode also greatly affects the Fano resonance feature in the scattering spectrum of the individual heterodimers. The molecular conductance at optical frequencies is estimated. The molecular junction-assisted electron tunneling is further verified by the reduced surface-enhanced Raman intensities of the molecules in the plasmonic nanocavity. We believe that our results provide an interesting system that can boost the investigation on the use of molecular junctions to modulate quantum plasmon resonances and construct molecular plasmonic devices.