Heterogeneous membrane structures exhibiting ion diode effects have attracted significant interest in energy conversion and storage. Herein, asymmetric double-layer graphene stacks with charged nanopores are constructed and placed in a KCl solution to study the controllable ion transport properties. Ion current rectification (ICR) is observed and the switching ratio is up to 102 by leveraging the asymmetric structure, charge, and interlayer distance. The trapping behavior of cations (K+) and anions (Cl−) in the nanochannels is investigated by applying bias voltages, and peak ion capture occurs at an electric field of E = 0.02 V/Å. The underlying mechanism of ICR is elucidated according to the dependence between the ion current and carrier concentration in the nanopores. The results provide valuable insights into the ICR mechanism and reveal high potential in the energy field.