In this study, the physicochemical properties and molecular interactions between zirconium-based metal-organic framework (UiO-66) and three different ionic liquids based on bis(trifluoromethanesulfonyl)imide anion (EMIM+, BMIM+ and OMIM+) was performed via a combined experimental and computational approach. The ionic liquid loaded UiO-66 or IL@UiO-66 was synthesized and characterized to understand the host-guest interaction. Density functional theory calculation was performed to analyse the electronic structure of IL@UiO-66 to provide molecular insight on the dominant interactions occurred in the hybrid material. Results showed that all ILs were successfully incorporated into the micropores of UiO-66. The 3D framework was retained even after loaded with ILs as analyzed from XRD pattern. FTIR spectrum reveals that interactions of ILs with UiO-66 influenced by the alkyl chain length of the cation. The anion has a profound affinity with the UiO-66 due to the presence of electronegative atoms. Phase transition study from DSC suggested that the incorporation of ILs has stabilized the framework of UiO-66 by shifting the endothermic peak to a higher state. These findings were further elaborated with DFT calculation. Geometrical optimizations confirmed the structural parameter changes of UiO-66 when loaded with ILs. These was mainly contributed by the non-covalent interactions which was confirmed by the reduced density gradient scattered plot. Another important findings are the strength of hydrogen bonding at the host-guest interface was influenced by the alkyl chain length. The molecular orbital analysis also shows that the size of alkyl chain influence the reactivity of the hybrid material. The present study provides fundamental insights on the molecular interaction of UiO-66 and ILs as a hybrid material, which can open new possibilities for advanced material for metal-organic framework applications in energy storage system, catalysis, gas storage and medicinal chemistry.