To prepare a cross-linked hybrid proton exchange membrane with high mechanical and oxidative stability, a silane monomer, namely 3-glycidoxypropyltrimethoxysilane (KH-560), is first grafted to sulfonated poly(arylene ether ether ketone)s bearing carboxyl groups (SPAEK-C) and hydrolysis–condensation is then performed on the grafted membranes to make them cross-link. 1 H NMR measurements and Fourier transform infrared spectroscopy are used to characterize and confirm the structures of SPAEK-Cs and hybrid polymer electrolyte membranes, respectively. The Si–O–Si cross-linking structure enhances the stability of the PEM greatly. The proton conductivities of the hybrid membranes with 5% KH-560 in weight reach 0.155Scm −1 at 80°C which is comparable to that of Nafion ® membranes. The ion-exchange capacity, water uptake and swelling, methanol permeability, mechanical properties are investigated to confirm their applicability in fuel cells.