Two‐dimensional (2D) nanochannels with confined spacing and tunable microenvironment exhibit broad application prospects in molecule‐scale processes. However, mass transport behaviors in nanochannels have yet been clearly elucidated, due to the complex physical and chemical structures of nanochannels. Herein, a series of vertically‐aligned nanochannels with tunable chemistry were fabricated by embedding graphene‐based lamellar membranes into epoxy matrix. In this way, 2 mm‐length robust nanochannels can maintain the molecular transport configuration throughout the membrane without the disturbance from entrance and cross‐layer domains. Based on these platforms, it is demonstrated that molecule–channel and molecule–molecule interactions codetermine molecular transport efficiency by controlling molecular configuration and transfer friction. Significantly, matched interaction energies permit fast transport with methanol permeance of over 26.1 L m−2 h−1 bar−1, which outperforms most reported long‐range nanochannels, while mismatched interaction energies fail to do so. In addition, the vertically‐aligned nanochannels membranes hold exceptional stability because of the mechanical protection of epoxy.