For designing better energy storage devices, the interfacial interaction between ILs and nanostructure is a prerequisite. In the present study, the interaction of ionic liquids such as [EMIm]+[X]− on Al12N12 and Al12P12 nanocages has been investigated using DFT theory. The complexes of Al12P12 nanocage exhibit higher values of adsorption energies than those of Al12N12. The adsorption energies of IL-complexes range from −38.9 to −63.6 kcal/mol. Non-covalent interaction (NCI) and quantum theory of atoms in molecules (QTAIM) analyses revealed non-covalent interactions between the ionic liquids and nanocages. NBO analysis shows charge transfer between the ionic liquids and Al12N12 and Al12P12 nanocages, which results in significant enhancement of dipole moment values of IL-complexes. [EMI]+ [X]−@Al12P12 complexes show higher dipole moment values than those of [EMI]+ [X]−@Al12N12 complexes. FMO analysis depicts a decrease in the HOMO-LUMO energy gap of IL-complexes, enhancing the electrical conductivity of these complexes. Furthermore, the calculated quantum molecular descriptors show that ILs adsorbed Al12N12 complexes are less reactive than ILs adsorbed Al12P12 nanocages. Thermodynamic properties revealed that the adsorption of ILs on Al12N12 and Al12P12 is an exothermic and spontaneous process. This study illustrates that the electronic properties of Al12N12 and Al12P12 nanocages are fine-tuned by the adsorption of ionic liquids. This study provides an efficient approach to design better electrode–electrolyte materials for super capacitors, fuel cells, ion batteries, and solar cells.