Two-dimensional (2D) nanofluidic systems provide a highly efficient way to integrate a huge amount of cascading lamellar nanofluidic channels into macroscopic membrane materials for practical use in, for example, molecular separation, water treatment, and energy storage. Besides the well-studied graphene-based materials, other 2D nanomaterials, such as the transition metal dichalcogenides (TMDCs), are expected as promising alternatives. Here, we report strong ionic current rectification (ICR) effect found in MoS2/WSe2 bi-layered membrane structure. The preferential direction for ion transport is from the WSe2 layers to the MoS2 layers. The maximum ICR ratio approaches 35 at intermediate electrolyte concentration. More intriguingly, by exchanging the deposition order of the MoS2 and WSe2 layers, the observed ICR effect can be reversed. These evidences justify that the highly rectified ion transport phenomenon results from the asymmetry in the reconstructed 2D layered materials. This work is the first discovery of ICR effect in 2D nanofluidic heterostructures, and provides further opportunities for innovative nanofluidic devices and materials.