An ultrathin polyion complex (PIC) layer containing β-cyclodextrin (β-CD) was formed on the surface of a charged base membrane. Thus, a positively charged copolymer containing β-CD was synthesized by the radical copolymerization of β-CD monomer and allylamine, and was used to modify the surface of a Nafion membrane containing negatively charged fixed ions. Electron spectroscopy for chemical analysis (ESCA) confirmed the presence of the copolymer on the surface of the Nafion membrane due to the formation of a PIC layer. The ability of the membrane to separate organic isomer mixtures was tested by the pervaporation technique, using butanol isomer mixtures as the feed model. The membrane exhibited a good selectivity toward butanol isomers, indicating the effectiveness of β-CD as a selective fixed carrier for the isomers.