Molecular dynamic simulations were performed to investigate the interfacial electric double layer (EDL) structure and differential capacitance (C d ) of ionic liquids (ILs), 1-ethyl-3-methyl-imidazolium bis(fluorosulfonyl)imide (EMIM+/FSI−) and 1-ethyl-3-methyl-imidazolium trifluoromethanesulfonate (EMIM+/Tf−) on planar graphite electrode. The differential capacitance curve (C d − U) of EMIM+/Tf− is asymmetric camel-shaped. The higher C d of EMIM+/Tf− than the EMIM+/FSI− at 0–0.5 V and 1.1–2.4 V, is attributed to the formation of a thinner EDL of EMIM+/Tf− induced by the smaller size of Tf− compared to FSI−. In addition, because of the fewer interaction sites between cations and Tf− with the more localized negative charge distribution, Tf− anions are expelled away from the charged electrode more easily, which makes more effective screening of EMIM+/Tf− to the charged electrode than that of EMIM+/FSI−. Accordingly, the C d of EMIM+/Tf− within the potential of −1.1 V to 0 V is higher than that of the EMIM+/FSI−. At highly negative potentials of −2.5 V to −1.1 V, FSI− with more interaction sites with cations are gradually squeezed out from the EDL, and more cations of EMIM+/FSI− accumulate to replace FSI−, leading to a higher C d of EMIM+/FSI− than EMIM+/Tf−. Meanwhile, the C d of EMIM+/Tf− decreases sharply due to the thicker EDL resulted from the overcrowded counterions.