The interactions of bovine serum albumin (BSA) with two alkylimidazolium-based ionic liquids, 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim]BF 4 ) and 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim]PF 6 ), in buffer solutions at pH 7.0 were investigated by isothermal titration calorimetry (ITC) and circular dichroism (CD). CD spectra showed that the two ionic liquids changed the secondary structure of BSA. Data process was based on the supposition that there were several independent types of binding sites on each BSA molecule for the two ligand molecules. The results obtained by using this supposition combined with Langmuir adsorption model showed that there were two types of such binding sites. One was the high affinity binding site, and the other was the low affinity binding site. The binding constants, changes in enthalpy, entropy and Gibbs free energy for the two types of binding were obtained, which showed that the two types of binding were driven by a favorable entropy increase. Furthermore, for either the ionic liquids, the number of the high affinity binding sites is much smaller than that of the low affinity ones. These results were interpreted with the molecular structure of BSA and the different substituent groups on imidazole ring of the two ionic liquid molecules.