The semi-interpenetrating polymer network (semi-IPN) based electrolyte membrane was synthesized from the poly(arylene ether ketone)-b-ketone sulfonated poly(arylene ether ketone) multi-block copolymer (PAEK-b-KSPAEK) and the organosiloxane organic-inorganic hybrid polymer network (OSPN) pre-synthesized. The chemical structure of the synthesized PAEK-b-KSPAEK and semi-IPN was identified using H-1 and F-19 nuclear magnetic resonance spectroscopy and Fourier transform infrared spectroscopy, and the dimension of the phase separated ionic clusters was examined by small angle X-ray scattering spectroscopy. Introduction of OSPN to PAEK-b-KSPAEK improved not only the thermal and mechanical stability (toughness) but also the oxidative stability. The performance of the membrane electrode assembly fabricated with the semi-IPN electrolyte membranes was superior to that of the pure block copolymer membrane because of the enhanced proton conductivity and toughness. While the semi-IPN24 membrane showed the comparable proton conductivity and cell performance to Nafion 115 membrane, its methanol permeability was significantly lower than that of Nafion 115 membrane.