Membranes with improved selectivity, stability, and non-fouling properties will be important in future chemical and waste treatment applications. Sulfonated poly(ether ether ketone)s (S-PEEKs) based membranes have been studied due to their good mechanical properties, thermal stability and ion exchange property. In this study, S-PEEKs based membranes were evaluated for ion exchange application. The microstructures of S-PEEKs membranes were studied by TEM and SAXS. The distribution of ion domains which mainly influence the properties of membranes was characterized. The fixed ion concentration, cation transport number and membrane selective permeability with different sulfonated degree or different micro structures were investigated. The relationship between the microstructures and properties of S-PEEK membranes was established. © 2005 Elsevier B.V. All rights reserved.