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A melt-extruded method has been used to prepare blend membranes of Perfluorosulfonic Acid Polymer (PFSA) and Perfluorocarboxylic Acid Polymer (PFCA) with different combination ratios. Fourier Transform Infrared (FT-IR) and X-ray Diffraction (XRD) analyses have showed that the chemical structure and crystallization behaviour of both polymers remained unchanged in the blend membrane, and the crystallinity has been increased for the blend membrane with a higher weight fraction of PFCA. According to the results obtained from Scanning Electron Microscope (SEM), PFSA and PFCA polymers are well compatible, forming mixed aggregates containing both sulphonyl and carboxyl ions. Surprisingly, a membrane containing a 50:50 ratio of PFSA/PFCA has showed microphase separation, and it possesses the smallest ionic cluster size among all the blend membranes prepared, as illustrated by the Small Angle X- Ray Scattering (SAXS) analysis. In addition, when the PFCA content was increased, the ion exchange capacity (IEC) for blend membranes remained the same, while their water uptake and proton conductivity have decreased rapidly. Compared with the PFSA/PFCA two-layered membrane, this PFSA/blend/PFCA membrane not only maintained respectable electrolysis property, also exhibited significantly higher peel strength, especially after the hydrolization process; plus, it has showed excellent resistance to the peeling damage under the operational conditions of chlor-alkali electrolytic cells. POLYM. ENG. SCI., 55:180–189, 2015. © 2014 Society of Plastics Engineers