Supported 2D layered materials are widely used in gas separation, water treatment, energy conversion, etc. In conventional viewpoint, the atop 2D membrane functions as an active layer for mass or charge separation in vapor or liquid phase, while the substrate membrane, containing aligned or tortuous 1D micro or nanoscaled fluidic channels, functions as a mechanical support. However, asymmetric transport property induced by the mixed‐dimensional composite structure is an equally very important, yet long‐overlooked element that endows new features to the membrane‐scale nanofluidic systems and contributes to the promotion of overall performance. Here, reported are asymmetric ion transport properties through 1D/2D nanofluidic heterojunction membrane (NFHM) under three different types of electrokinetic driving force. The 1D/2D NFHM comprises of self‐assembled graphene oxide multi‐layers (2DM, negatively charged) supported on a polydopamine‐coated 1D nanopore array (1DM, ampholytic). Intriguingly, it is found that the preferential direction for electric‐field‐driven ionic transport is from the 2DM to the 1DM, while under the concentration difference or the hydraulic flow, the preferred direction for diffusion or streaming ionic current goes in the reversed direction, from the 1DM to the 2DM. A theoretical model based on coupled Poisson–Nernst–Planck and Navier–Stokes equations is employed to explain the asymmetric ion transport phenomena.