The gas-phase ion pairs of the ionic liquids containing 1-ethyl-3-methylimidazolium ([emim](+)) and 20 natural amino acids ([AA](-)) are studied at the B3LYP/6-311+G (d,p) level. The optimized structures, energies, and natural population analysis are presented and analyzed in terms of their possible correlation with the interaction energies and the H-bond separations. It is found that all the ion pairs of [emim][AA] call form strong H-bond interactions, which are dominated by the side-chain structure and the functional group of amino acid anions. The calculations indicate that an increase of the alkyl side-chain length coincides with a gradual decrease of H-bond energy, while the functional groups lead to the different localized charges on the anions, consequently affecting the electrostatic force. In addition, the intramolecular H bond in [AA](-) can weaken the interaction, due to the decrease of the proton-accepting ability of the carbonyl O atoms. The H-bond chemical nature of [emim][AA] is investigated by atoms in molecules and natural bond orbital analyses. The preliminary analysis of 20 kinds of [emim][AA] ion pairs provides some initial hints as to the relationship between the interaction energy and the experimental glass transition temperature.