In this article, we have compared the anions of sodium salts (Is) and ionic liquids (ILs) with the stability and structure of α-chymotrypsin (CT), through fluorescence, thermal fluorescence analysis and circular dichroism (CD) spectroscopy. The experimental results revealed that the Hofmeister series of anions such as SCN⁻, SO₄²⁻, Cl⁻, Br⁻, CH₃COO⁻ and I⁻ of Is destabilized the native structure of CT. On the contrary, the anions such as CH₃COO⁻, Cl⁻ and Br⁻ of imidazolium-based IL with a fixed cation such as 1-butyl-3-methylimidazolium, [Bmim]⁺, stabilized the native structure of CT. The remaining anions of ILs such as SCN⁻, HSO₄⁻, and I⁻ acted as denaturing agents for the native structure of CT. Furthermore, molecular docking results show that the imidazolium-cation of the IL enters the sub-domains of CT and interacts with the ionic residues of CT, that is, Ser217 close to Trp215. This interaction is in well agreement with the fluorescence quenching observed for CT in the presence of [Bmim]⁺. On the other hand, the destabilizing anion such as SO₄²⁻ was observed to be directly interacting with Ser195 in the active site of CT. We have observed that the Hofmeister series effects of anions of either Is or ILs are entirely based on the interaction of the anions with their counterions, that is, cations, with solvent molecules, as well as with the protein surface. Evidently, these interactions vary with the co-solvent system and the type of protein. Hence, the stability of a biomolecule in the presence of the anions may or may not obey the Hofmeister series.