Vibrational spectroscopy is a powerful tool for studying the microstructure of liquids, and anatomizing the nature of the vibrational spectrum (VS) is promising for investigating changes in the properties of liquid structures under external conditions. In this study, molecular dynamics (MD) simulations have been performed to explore changes in the VS of 1-ethyl-3-methylimidazolium hexafluorophosphate ([Emim][PF6]) ionic liquid (IL) under an external electric field (EEF) ranging from 0 to 10 V•nm −1 at 350 K. First, the vibrational spectra for [Emim][PF6] IL as well as its cation and anion are separately obtained, and the peaks are strictly assigned. The results demonstrate that the VS calculated by MD simulation can well reproduce the main characteristic peaks in the experimentally measured spectrum. Then, the vibrational spectra of the IL under various EEFs from 0 to 10 V•nm −1 are investigated, and the intrinsic origin of the changes in the vibrational bands (VBs) at 50, 183, 3196, and 3396 cm −1 is analyzed. Our simulation results indicate that the intensities of the VBs at 50 and 183 cm −1 are enhanced. In addition, the VB at 50 cm −1 is redshifted by about 16 cm −1 as the EEF is varied from 0 to 2 V•nm −1 , and the redshift wavenumber increases to 33 cm −1 as the EEF is increased to 3 V•nm −1 and beyond. However, the intensities of the VBs at 3196 and 3396 cm −1 show an obvious decrease. Meanwhile, the VB at 3396 cm −1 is redshifted by about 16 cm −1 when the EEF increases to 3 V•nm −1 , and the redshift increases to 33 cm −1 with an increase in the EEF beyond 4 V•nm −1 . The intensity of the VB at 50 cm −1 increases because of the increase in the total dipole moment of each anion and cation (from 4.34 to 5.46 D), and the redshift is attributed to the decrease in the average interaction energy per ion pair (from −378.7 to −298.0 kJ•mol −1 ) with increasing EEF. The intensity of the VB at 183 cm −1 increases on account of the more consistent orientations for cations in the system with increasing EEF. The VB at 3196 cm −1 weakens visibly because a greater number of hydrogen atoms appear around the carbon atoms on the methyl/ethyl side chains and the vibrations of the corresponding carbon-hydrogen bonds are suppressed under the action of the EEF. Furthermore, the intensity of the VB at 3396 cm −1 decreases due to the decrease in the intermolecular + C-H···F − hydrogen bonds (HBs), while the relaxation effect that is beneficial for the formation of HBs simultaneously exists in the system under the varying EEF, thus causing a redshift of the VB at 3396 cm −1 .