We systematically investigate the binding nature of CB towards 20 amino acids in both neutral (AAs) and protonated (AAs+) states by quantum chemistry methods. The result indicates molecular recognition process are enthalpy-driven. Among AAs, Arg and Asn shows the largest binding strength to CB, and for AAs+, Gln+ and Asn+ bind to CB the strongest. The binding strength of protonated CB/AA+ is much stronger than that of neutral CB/AA counterpart, due to the introduction of ion-dipole interaction and the increase number and strength of hydrogen bonds. Energy decomposition analysis (EDA) indicates that electrostatic interactions play major roles in both CB/AAs and CB/AAs+ complexes. Moreover, we analyzed the dependence of binding strength on single AA volume and dipole moment. This study is benefit for providing valuable information in predicting the recognition sites for sequence-based peptide or protein by CB and rationally designing synthetic host molecule for specific peptide or protein recognition.