Ionic liquids, emerging as innovative solvents for energy harvesting, necessitate a comprehensive understanding of their structural characteristics at the graphene-ionic liquid interface. This work delves into the effects of external electric fields (EEFs) on the polarization and vibrational spectrum of 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([Emim][NTf2]) on a graphene surface, employing density functional theory calculations. The analysis reveals that the geometrical configuration and stability of functional groups within the graphene-[Emim][NTf2] system are influenced by both the direction and intensity of the applied EEF. Notably, the threshold EEF strength required for dissociation varies based on the structural configuration of the anion. The electronic energy, dipole moment, and polarization rate under varying EEF conditions have been quantitatively assessed, providing insights into their EEF-dependent behaviors. Utilizing the independent gradient model approach, the inter-ion interactions, such as hydrogen bonding and van der Waals forces, under the influence of EEFs were analyzed, and how these interactions evolve with changes in the direction and intensity of the EEFs were also explored. Furthermore, the vibrational spectrum of [Emim][NTf2] on the graphene surface, spanning a range of 10–3500 cm−1, was meticulously calculated to systematically investigate the impact of the EEF on the vibrational spectra of the graphene-[Emim][NTf2] system. A key finding of this work is the distinct shifts in the vibrational peaks of the cis and trans isomers of [NTf2]− on the graphene surface, which can be attributed to differences in their exchange energies. Specifically, the exchange energy for the cis isomer of [NTf2]− is measured at 107.43 kJ∙mol−1, in contrast to 98.51 kJ∙mol−1 for the trans isomer.