To compare 1-butyl-3-methylimidazolium ([BMIM](+))- and 1-butyl-3-methylpyridinium ([BMPy](+))-based ionic liquids (ILs) and investigate the influence of intramolecular and intermolecular interactions on physicochemical properties, a systematic study was performed on the electronic structures and physicochemical properties of [BMIM](+) tetrafluoroborate ([BMIM][BF4]), [BMIM](+) hexafluorophosphate ([BMIM]-[PF6]), [BMIM](+) hydrogen sulfate ([BMIM][HS0(4)]), [BMIM](+) methylsulfate ([BMIM][MSO4]), [BMIM](+) ethyl-sulfate ([BMIM][ES0(4)]), [BMPy] (+) tetrafluoroborate ([BMPy] [BF4]), [BMPy](+) hexafluorophosphate ([BMPy][PF6]), [BMPy](+) hydrogen sulfate ([BMPy][HSO4]), [BMPy](+) methylsulfate ([BMPy][MSO4]), and [BMPy](+) ethylsulfate ([BMPy][ESO4]) using density functional theory and molecular dynamics simulation. The results reveal that aggregation behavior exists in [HSO4](-)- and [ESO4](-)-based ILs, and the differences between their densities and self-diffusion coefficients are smaller when there is an aggregation effect in ILs. A dimer is formed by two strong hydrogen bonds between two [HSO4](-) anions in [HSO4]-based ILs, and the existence of hydrogen bonds in ILs increases density and decreases the self-diffusion coefficient. The intermolecular interaction strength of [BMIM](+)-based ILs is stronger than that of [BMPy](+)-based ILs.