Molecular dynamics simulation is employed to study graphene supercapacitors. Four different ionic liquids are considered as an electrolyte, each of which is combination of the same cation 1-ethyl-3-methylimidazolium([emim]+), and different, cyano-containing anions, thiocyanate ([SCN]–), dicyanamide ([N(CN)2]–), tricyanomethanide ([C(CN)3]–), and tetracyanoborate ([B(CN)4]–), respectively. In particular we investigate how electric double layer structure and electrical properties are affected by the structure of cyano containing anions. Cations and anions make alternating structure near charged electrode. Differential capacitances in four ionic liquids are found to have a maximum value at negative potential. The maximum capacitances are comparable to each other, but the corresponding potential shifts to the negative side as more cyano groups are attached to the anion. Starting from the interfacial layer, the effects of the further ionic layers on differential capacitance are systematically investigated. Comparing charges of the electrode and those of ionic layers, we find that differential capacitance behavior mainly stems from the ion exchange between electric double layer and bulk region. The ion exchange behaviors are decomposed into cation and anion contributions. The differential charging mechanisms of the system are strongly dependent on the electric potential. The maximum capacitances are consequence of rapid desorption of respective anions.