The proline cation based amino acid ionic liquid [Pro](+)[NO3](-) was systematically studied by density functional theory at the B3LYP/6-311+-1-G** level. The stable geometries of the cation, anion, ion pair, as well as the ion-pair dither [Pro](2)(+)[NO3](2)(-) with no imaginary frequencies were obtained and characterized. In the single [Pro](+)[NO3](-) unit, proton transfer from [Pro](+) to [NO3](-) can be observed in some of the configurations and the corresponding proton-transferred products (neutral pairs) are strongly hydrogen bonded. While in the ion-pair dimer [Pro](2)(+)[NO3](2)(-), proton transfer does not occur and the components are stabilized by ionic interaction and hydrogen bonding interaction jointly. The proton transfer reaction between the cation and the anion in the single ion-pair unit has been investigated, and the role that the proton transfer reaction may play in the physicochemical property change of the ionic liquids has also been discussed. The interactions in the single ion-pair unit [Pro](+)[NO3](-) and in the ion-pair dither [Pro](2)(+)[NO3](2)(-) were both carefully studied. The hydrogen bonds (H bonds) between the various fragments were analyzed by the atoms in molecules theory and harmonic vibrational frequency.