Nanofilms that can fast permeate solvents and accurately sieve molecules are of significant importance for separation. A promising strategy is to align the inner cavities of macrocycles into the channels within nanofilms, and control the channel size by selecting the macrocycles. However, the channels outside the macrocycles are ignored. Here, we prepare nanofilms with hydrophobic channels (cyclodextrin inner cavity) and hydrophilic channels (cyclodextrin outer space) through interfacial polymerization of azobenzene-4,4’-dicarbonyl dichloride and amino-functionalized β-cyclodextrin. By utilizing the significant geometric changes caused by the photoisomerization of azobenzene, nanofilms with adjustable hydrophilic channel sizes were obtained. Our nanofilms have high permeability to polar and non-polar solvents, and can distinguish molecules with almost the same molecular weight but different shapes. This work expands the development of next-generation nanofilms generated through interfacial polymerization by incorporating rational molecular design.