Due to their unique properties, ionic liquids (ILs) have attracted the academic and industrial attentions. However, recent controversies have focused on what are the main forces to determine the behaviors of ILs. In this work, a detailed DFT calculation was carried out to investigate the intermolecular interactions in two typical ILs, [Emim][BP4] and [Bmim][PF6]. The results indicate that hydrogen bonds (H-bonds) are the major intermolecular structural feature between cations and anions. Although the electrostatic force remains the major noncovalent force (70% of the total energy by energy decomposition calculation), the interaction energies calculated at different theoretical levels indicate that H-bond and van der Waals interactions cannot be ignored. However, the H-bonded capacities from natural bond orbital (NBO) delocalization energies do not show the consistent;flanges in the total interaction energies and number of H-bonds. Based on the canonical orbitals analysis, it is found that the sigma-type orbital overlap and the partial charges transfer between anion and cation, finally, result in the significant energy reduction and rationalize the preferable location of anion, which is an essential understanding for the interaction and structure in the ion pair. Additionally, the strong agreement between the experimental IR spectra and the calculated vibrations implies that the structures of the larger ion clusters provide a reasonable depiction for bulk ILs at room temperature condition.