Brønsted acidic ionic liquids (BAILs) are clean and versatile replacements for traditional homogeneous acid catalysts and have attracted much attention as efficient catalysts for the synthesis of valuable chemicals. It’s critically important to understand the structural properties of BAILs from the molecular level. In this work, we studied a series of −SO3H functionalized acidic ionic liquids by density functional theory (DFT) calculations, and the most stable geometries were obtained by global semiempirical quantum mechanical search. The most stable structures of cations are formed when more intramolecular H-bonds exist. For BAILs clusters, intramolecular and intermolecular H-bonds coexist and play a critical role in the stability of the system. The interaction energy decreases with increasing alkyl chain length. When the alkyl chain was replaced by −SO3H groups, the interaction energy increased due to more H-bonds formed with the anions. The quasi-3D network is formed in the BAILs clusters and the electrostatic interaction plays a critical role in stabilizing the ion clusters. This work helps to understand the microcosmic interactions of BAILs in-depth and design them in a “task-specific” way.