The intermolecular interactions of imidazolium- and cholinium-based ionic liquids and hen egg-white lysozyme (HEWL) were studied by spectral, thermodynamic, and computational methods. The cholinium- and imidazolium-based ionic liquids: choline chloride [Ch][Cl], choline dihydrogenphosphate [Ch][DHP], choline acetate [Ch][OAc], 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF4], 1-butyl-3-methylimidazolium trifluoromethanesulfonate [BMIM][TfO], 1-butyl-3-methylimidazolium acetate [BMIM][OAc] and 1-butyl-3-methylimidazolium methanesulfonate [BMIM][CH3SO3] were selected. The proton donor and acceptor abilities of ionic liquids were determined based on gas chromatography and solution calorimetry data. The temperature denaturation of HEWL in ionic-liquid solution was observed using capillary differential scanning calorimetry (DSC) and circular dichroism spectroscopy (CD). The interaction of ionic liquids with HEWL at the standard temperature was accessed by monitoring the protein’s fluorescence changes. The effect of the ionic liquid on the stability of the native structure of HEWL strongly depends on the proton acceptor ability of ionic liquids. The denaturation temperature of the native structure HEWL is linearly correlated with the enthalpy of the specific interaction (hydrogen bonding) of methanol and trichloromethane in the studied ionic liquids. At the same time, fluorescence data revealed ionic liquid-specific effects, which depend on both ions in the ionic liquid. Both fluorescence and molecular docking data indicate a lack of strong binding between the studied ionic liquids and HEWL.