Nanofluidic diodes are potentially useful in many important applications such as sensing, electronics, and energy conversion. However, the manufacturing of controllable nanopores for nanofluidic diodes is technically challenging. Herein, a nanofluidic diode is designed from a highly programmatic covalent organic framework (COF). Through molecular simulation, remarkable diode behavior is observed in a hybrid-bilayer COF but not in its constituent single-layer COFs. The rectification effect of ion current in the hybrid-bilayer COF is attributed to an asymmetric electrostatic potential across the COF nanopore. Furthermore, a synergistic effect of counterion is unraveled in the hybrid-bilayer COF, and the presence of counterion is found to reduce the entry barrier and facilitate ion transport. The performance of the hybrid-bilayer COF as a nanofluidic diode is comprehensively investigated by varying salt concentration, layer number, interlayer spacing, and slipping. This proof-of-concept simulation study demonstrates the feasibility of the hybrid-bilayer COF as a nanofluidic diode and the finding may stimulate the development of new nanofluidic platforms.