Multi-block and random copolymers based on poly(arylene ether ketone) are synthesized. The chemical structure of the hydrophobic and hydrophilic oligomers and the copolymers synthesized from them is identified using 1H - and 19F- nuclear magnetic resonance (NMR) spectroscopy, attenuated total reflection fourier transform infrared (ATR-FTIR) spectroscopy, and gel permeation chromatography (GPC). The development of distinguished hydrophobic-hydrophilic phase separation is confirmed by small-angle X-ray scattering (SAXS) spectroscopy. The proton conductivity and water uptake along with the thermal, mechanical, oxidative stabilities are measured to investigate the effect of the copolymer structure on the membrane properties. While water uptake is similar with respect to each other, the proton conductivity of the multi-block copolymer membrane is higher than that of random one at the same levels of IEC. It results from much more distinct hydrophobic-hydrophilic phase separation formed in the multi-block copolymer membrane than the random one. The ion cluster dimension of the multi-block copolymer membranes is larger than that of the random copolymer membranes from the SAXS analysis. Also, the ion cluster dimension distribution of the block copolymer membranes is much narrower than that of random ones. The multi-block copolymer membranes illustrate superior oxidation stability to the random copolymer membrane due to the same phase separation difference.