The capacitance of carbon electrodes can be enhanced by tuning nanoscale roughness of the electrode surface, which facilitates separation between cations and anions within the electrical double layer. As the extent of ion separation depends on the ion correlation of bulk electrolytes, it is expected that the intrinsic electrical properties of ionic liquids (ILs) will also influence the double-layer structure and capacitance at nanostructured electrode interfaces. In this work, we use constant voltage molecular dynamics simulations to investigate the differential capacitance profiles for three different ionic liquids at model graphene electrode with subnanometer scale surface roughness. We focus on the ionic liquids composed of 1-butyl-3-methylimidazolium (BMIm+) cations and bistriflimide (TFSI–), triflate (OTf–), or tetrafluoroborate (BF4 –) anions. Surprisingly, we find that [BMIm+]­[TFSI–] exhibits significantly enhanced differential capacitance at high positive potential compared to [BMIm+]­[BF4 –] and [BMIm+]­[OTf–] with smaller anions. We demonstrate that this unexpected capacitance trend is due to nonpolar interactions between trifluoromethyl groups of TFSI– anions that promote TFSI–/TFSI– pairing at the electrode interface. These anion pairs lead to significantly reduced BMIm+ density in the [BMIm+]­[TFSI–] double layer compared to the other two ionic liquids. By contrast, no anion pairing occurs for [BMIm+]­[BF4 –] and [BMIm+]­[OTf–] at the same voltage regime, so nonpolar alkyl groups of BMIm+ cations still predominantly accumulate at the nanostructured electrode interface, resulting in only slight enhancement of capacitance due to the surface roughness effect. This physical insight is important for controlling IL interfacial structure to enhance the capacitance of nanostructured electrodes.