We report a technique that can be utilized as a nanoscale thermometer and its application to metal-molecule-metal junctions at room temperatures. We find that a molecular junction heats up to 463 K at 1 V. We also revealed an onset bias of approximately 0.04 V for heat generation via electron-phonon scattering by examining inelastic electron tunneling spectroscopy. The present results suggest the importance of attaining an optimal thermal link at molecule-electrode interfaces for providing practically sufficient electrical durability.