Ten kinds of alkylimidazolium-based aprotic ionic liquids (AILs) with hydrogen carbonate, dihydrogen phosphate, and hydrogen sulfate anions were prepared, and methods of elemental analysis, infrared spectroscopy, and proton nuclear magnetic resonance were employed to characterize the ILs, respectively. Properties such as electrical conductivity, density, dynamic viscosity, surface tension, were measured and correlated with thermodynamic and empirical equations over various temperature ranges under ambient conditions. Some significant thermodynamic parameters of the ILs were estimated. The trends of changing with temperature for the dynamic viscosity and the electrical conductivity were described by the Vogel-Fulcher-Tamman equation. The activation energies of dynamic viscosity and electrical conductivity were also calculated. Further, the structures and the energetics of the ILs ions were obtained through combining density functional theory calculations and the COSMO-RS methodology. The structural effects of ion variation on the properties of the ILs were studied.