Scanning tunneling microscopy (STM) vibronic spectroscopy, which has provided submolecular insights into electron-vibration (vibronic) coupling, faces challenges when probing the pivotal low-frequency vibronic excitations. Because of eigenstate broadening on solid substrates, resolving low-frequency vibronic states demands strong decoupling. This work designs a type II band alignment in STM junction to achieve effective charge-transfer state decoupling. This strategy enables the successful identification of the lowest-frequency H
g
(ω
1
) (Raman-active H
g
mode) vibronic excitation within single C
60
molecules, which, despite being notably pronounced in electron transport of C
60
single-molecule transistors, has remained hidden at submolecular level. Our results show that the observed H
g
(ω
1
) excitation is “anchored” to all molecules, irrespective of local geometry, challenging common understanding of structural definition of vibronic excitation governed by Franck-Condon principle. Density functional theory calculations reveal existence of molecule-substrate interfacial charge-transfer dipole, which, although overlooked previously, drives the dominant H
g
(ω
1
) excitation. This charge-transfer dipole is not specific but must be general at interfaces, influencing vibronic coupling in charge transport.