In this work, the structures of the -SO3H functionalized acidic ionic liquid 1-(3-sulfonic acid) propyl-3-methylimidazolium hydrogen sulfate ([C(3)SO(3)Hmim]HSO4), including its precursor compound (zwitterion), cation, and cation-anion ion-pairs, were optimized systematically by the DFT theory at B3LYP/6-311++G** level, and their most stable geometries were obtained. The calculation results indicated that a great tendency to form strong intramolecular hydrogen bonds was present in the zwitterion, and this tendency was weakened in the cation that was the protonation product of zwitterion. The intramolecular hydrogen bonds and intermolecular hydrogen bonds coexisted in the ionic liquid, and they played an important role in the stability of the systems. The strongest interaction in the ionic liquid was found between the anion and the functional group. The transition state research and the intrinsic reaction coordinate analysis of the hydrogen transfer reaction showed that, when the cation and the anion interacted near the functional group by double O-H center dot center dot center dot O hydrogen bonds, the ionic liquid was inclined to exist in a form of the zwitterion and H2SO4.