Lamellar membranes with well‐defined 2D nanochannels show fast, selective permeation, but the underlying molecular transport mechanism is unexplored. Now, regular robust MXene Ti3C2Tx lamellar membranes are prepared, and the size and wettability of nanochannels are manipulated by chemically grafted hydrophilic (−NH2) or hydrophobic (−C6H5, −C12H25) groups. These nanochannels have a sharp difference in mass transfer behavior. Hydrophilic nanochannels, in which polar molecules form orderly aligned aggregates along channel walls, impart ultrahigh permeance (>3000 L m−2 h−1 bar−1), which is more than three times higher than that in hydrophobic nanochannels with disordered molecular configuration. In contrast, nonpolar molecules with disordered configuration in both hydrophilic and hydrophobic nanochannels have comparable permeance. Two phenomenological transport models correlate the permeance with the mass transport mechanism of molecules that display ordered and disordered configuration.