A simple and effective strategy to simultaneously enhance the permeability and antifouling properties of ethylene vinyl alcohol (EVAL) membrane was developed based on the bioinspired natural cleaner, cilia. Taking clue from the self-cleaning effect of cilia, supramolecular polyrotaxanes (PRs) with sliding and rotating cyclic molecules along linear chains were synthesized using azide-alkyne click chemistry. Cilia-like PRs were incorporated into EVAL matrix in the fabrication of modified EVAL membranes. Cilia-like structures protruding from the membrane surface have been observed by SEM, TEM and AFM. By imitating natural ciliary movements, these structures provided a proactive self-cleaning system to remove the foulants. The introduction of cilia-like PRs enhanced the surface roughness and hydrophilicity, and significantly enhanced permeability by 55.3% compared to raw EVAL membrane. Moreover, the membrane modified with cilia-like PRs showed an excellent antifouling property with a lower water flux decline (12.6%) and higher water flux recovery (94%) in dynamic fouling tests. Furthermore, this modified membrane develops the scope of bioinspired membranes, inspiring more attractive potential applications in self-cleaning materials, dynamic membranes and supramolecular machines.