This work reveals the capacitive behaviors of graphene nanomaterials in typical ionic liquids of [BMI+] [BF4
−] using molecular dynamics simulations. It is found that the charging process induces a structural transition from disordered to partially ordered and then ordered multilayer structures of [BMI+][BF4
−] electrolyte, yielding a multiple layer-by-layer packing structure of BMI+ cation and BF4
− anion. Especially, a counterion-adsorption-dominated Helmholtz layer is revealed at a high charge density of 16 μC/cm2, which is primarily responsible for the superior capacitance results. Besides, the differential capacitance of [BMI+][BF4
−] exhibits a symmetric convexity-shaped curve, showing a maximal capacitance value of 4.83 μF/cm2. The as-obtain simulation results help to understand the microscopic charge storage mechanisms of graphene in ionic liquids.