The microstructure of electrical double layers (EDLs) of 1-butyl-3-methylimidazolium tetrafluoroborate ([Bmim]BF4), 1-butyl-3-methylimidazoliumhexafluorophosphate ([Bmim]PF6), and 1-butyl-3-methylimidazoliumbis (trifluoromethylsulfonyl) imide ([Bmim]TFSI) were studied by quantum chemical calculation and molecular dynamics simulation. For the set of ionic liquids investigated here, we found some interesting universal laws due to differences geometry and electronic structure of anions. We show that the morphology of the three anions on the electrode surface is different due to the different geometric structure. The plane formed by the bottom three atoms of the symmetrically tetrahedral BF4- and the bottom atom of the symmetrically octahedral PF6- face the electrode whether the electrode is charged or not, while the conformation of twisted V-shaped TFSI- changes with different surface charges on the electrode. Meanwhile, we also demonstrate that the energy of highest occupied molecular orbital (EHOMO), the energy of lowest unoccupied molecular orbital (ELUMO) and their energies gap (ΔE) are very interesting due to different electronic structure of anions. Specially, the EHOMO, ELUMO, and ΔE were related to the electronegativity of the central atom in the case of the same symmetry on the neutral surface. The more electronegative the central atom is, the lower EHOMO, ELUMO and higher ΔE values are. However, on the charged surface, the interaction between anion and electrode is opposite to ΔE. Moreover, different arrangements of anion and cation are related to the interaction between particles. The stronger interaction leads a double-row structure and the weak interaction lead worm-like and island patterns on Au (100) surface. In general, we observed that the higher ΔE cause stronger interaction, which lead to different patterns on Au (100) surface. Meanwhile, we also confirmed that the stronger interaction between particles and electrode lead to the thinner effective EDL and a large differential capacitance value. These results provide a new perspective for double-layer structure in atomic and molecular level. This is helpful to deepen the understanding of the interface phenomena and characteristics of [Bmim]BF4, [Bmim]PF6, and [Bmim]TFSI on Au (100) system and provide theoretical basis for the application of these kind of systems.