The interactions between a Cu-based metal-organic framework (MOF), Cu-BTC, and an ionic liquid (IL), 1-ethyl-3-methylimidazolium ethyl sulfate, were studied by employing density functional theory (DFT) calculations and vibrational spectroscopy. The Fourier transform infrared (FTIR) and Raman spectra show that the confinement of the IL in the MOF has significant impact on the structure of the MOF as well as on the IL. Raman spectra and DFT calculations reveal a perturbation of the symmetry of the MOF structure due to the interaction of the IL anion with the Cu ions. FTIR and Raman spectra show that the molecular interactions in turn influence the structure of the ion pair. Inside the MOF, two different types of structure of IL ion pairs are formed. One ion-pair structure exhibits enhanced interionic interactions by strengthening the hydrogen bonding between cation and anion, whereas the other structure corresponds to weaker interactions between the IL cation and anion. Moreover, it is shown that the IL imidazolium ring can directly interact with either the MOF or the anion. The difference electron density analysis by DFT calculations indicates that molecular interactions of MOF and IL are accompanied by a transfer and redistribution of electron density.