<p indent=0mm>Supercapacitor, an advanced energy-storage technique based on ion electrostatic adsorption at the solid–liquid interface, exhibits fast charge–discharge rates, high power density, high rate ability, and long cycle life. Two-dimensional nanomaterials (e.g., graphene) and room-temperature ionic liquids (RTILs) have been considered potential electrode and electrolyte candidates, respectively, for supercapacitors. However, their high concentration, nanosized confined space, and complex molecular structure/intermolecular interactions make the ion packing structure and electrosorption process substantially different from that in conventional dilute electrolytes (e.g., aqueous solution and organic electrolyte) near the nonconfined space, which cannot be interpreted by the Gouy–Chapman–Stern model and Debye–Huckel approximation based on the continuous medium hypothesis. In this study, molecular dynamics simulations are employed to comprehensively explore the in-depth mechanisms of ion distribution at equilibrium and ion transport at nonequilibrium within the multilayer graphene nanochannel/RTILs system. The ion layer structure and its number density inside the graphene nanochannels are significantly enhanced compared with the nonconfined graphene plane. Moreover, the position of counter-ion within the graphene nanochannel is much closer to the charged wall, indicating better charge-storage capability. These phenomena are mainly attributed to the more prominent interactions between graphene and ions inside the confined space. In addition, the ion transport behaviors inside the graphene nanochannel are strongly dependent on the electrode potential and channel widths. In particular, an anion adsorption-dominated charging mechanism is recognized on the graphene plane, whereas confined graphene nanochannels exhibit more complex ion transport behaviors, i.e., the anion adsorption-dominated and cation desorption-dominated behaviors alternate with increasing potential. The ion transport mechanism is highly related to the confinement, potential, ion–ion interaction, and ion–electrode interaction. Finally, an interfacial ion transport model based on nonequilibrium thermodynamics theory is proposed to analyze the real-time flux of anions and cations within the electrodes in the nonequilibrium state. It is found that the decreased charge storage at high charge–discharge rates is mainly attributed to the significant hindrance of co-ion transport, which is quite different from the traditional view (i.e., the hindrance/hysteresis of counter-ion adsorption). Such a phenomenon can be interpreted as follows. First, the transient formation of crowded counter-ions and dilute co-ions inside the graphene nanochannel leads to slower transport of the co-ions. Second, the decreasing number density of co-ions inside the graphene nanochannel also hinders the flux of co-ions in and out of the electrode. These insights reveal the energy and mass transfer mechanisms during the electrostatic adsorption process within complex graphene nanochannel/RTILs systems, which can potentially guide the design and fabrication of electrode materials and electrolytes for high-performance supercapacitors.