Display omitted •Anodic alumina membranes modification performed using octadecylphosphonic acid.•Surface modification was proved by IR- and Raman spectroscopy and thermal analysis.•Modification allows to control molecule residence time in adsorbed stage.•For hydrocarbons TMAC coefficients depend on surface saturation of grafted layer.•Modification allows to achieve n-C4H10/CH4 separation factors up to 32.3. Here we report evidence for substantial changes in the separation efficiency of nanoporous anodic alumina membranes with nanochannel diameters ranging from 10–100 nm modified with octadecylphosphonic acid in the transitional flow regime. Softening of surface by alkyl groups with a surface density ∼2 groups/nm2 leads to a general permeance decrease in 3–500 times, depending strongly on the penetrant gas nature and the channels diameter. The divergence of the permeance, for different gases, increases with the decreasing diameter of the pores. For a surface-functionalized membrane, with 10-nm channel diameters, it results in n-C4H10/CH4 ideal and mixed gas separation factors up to 32.3 and 9.0 respectively at a n-C4H10 permeance up to 3.5 m3/(m2·bar·h). The effect is related to the changes of the ratio of molecule travelling time to residence time in the adsorbed state, as well as a strong influence of surface saturation by the absorbed molecules on the tangential momentum accommodation coefficient, which is supported by the derived model. Synergetic contribution of these two factors allows to enhance the separation factor of permanent and condensable gases strongly beyond the Knudsen limit, while maintaining a high permeance of porous membranes.