A symmetrical graphene-based supercapacitor is constructed for studying the charge-transfer mechanism within the graphene-based electrodes using both experiment measurements and molecular simulation. The in-house synthesized graphene is characterized by XRD, SEM and BET measurements for morphology and surface area. It is observed that the electric capacity of graphene electrode can be reduced by both high internal resistance and limited mass transfer. Computer modeling is conducted at the molecular level to characterize the diffusion behavior of electrolyte ions to the interior of electrode with emphasis on the unique 2D confinement imposed by graphene layers. Although graphene powder poses a moderate internal surface of 400 m2 g−1, the capacitance performance of graphene electrode can be as good as that of commercial activated carbon which has an overwhelming surface area of 1700 m2 g−1. An explanation to this abnormal correlation is that graphene material has an intrinsic capability of adaptively reorganizing its microporous structure in response to intercalation of ions and immergence of electrolyte solvent. The accessible surface of graphene is believed to be dramatically enlarged for ion adsorption during the charging process of capacitor.