Abstract In order to improve selective inclusion of cyclodextrin (CD) and permeate flux, separation of structural isomers ( o -, m - and p -nitrophenols) and optical isomers ( d - and l -phenylalanines) were conducted using some modified α and β-CDs, glucosyl (G1)-, maltosyl (G2)-, hydroxy-propyl (HP)-, α- and β-CDs, according to the previously proposed separation method. Generally, rejections of the modified CD are more enhanced than parent α-CD and β-CD by YM1 (molecular weight cut-off (MWCO) of 1000 Da), PLBC (MWCO of 3000 Da) and YM5 (MWCO of 5000 Da) membranes. The G2-β-CD and HP-β-CD are rejected perfectly by YM1 membrane. Rejections of the modified CDs by PLBC and YM5 membranes decrease by more than 20% of those of the YM1 membrane. The selectivities of p -nitrophenol to o - or m -nitrophenol are enhanced with more modified α-CDs by YM1 membrane than those of parent α-CD. The selectivities decrease the PLBC and YM-5 membranes sharply. However, no enhancement occurs in the selectivities with modified β-CDs. l -phenylalanine is included, which is stronger than d -phenylalanine with all modified β-CDs. Their selectivities are higher than that of the parent β-CD. We proposed a new recycle system of isomers separation based on these data to apply the method for practical use.