The effects of three-dimensional cubic (Im3m) structured mesoporous benzene–silica materials inside a sulfonated poly(ether ether ketone) (sPEEK) polymer matrix are investigated for application as proton exchange membranes in a direct methanol fuel cell (DMFC) system. Cubic (Im3m) structured mesoporous benzene–silica is prepared in the presence of a Pluronic F127 PEO-PPO-PEO template under acidic conditions and sulfonated with ~98% sulfuric acid using a post-grafting method. The sulfonated mesoporous materials are mixed with a sPEEK (65% of sulfonation degree) polymer matrix using a solvent casting method. These composite membranes exhibit much lower methanol crossovers (3.0~–5.0×10 −7 cm 2 s −1 ) than a commercial Nafion®117 membrane (1.6×10 −6 cm 2 s −1 ). Additionally, the composite membranes exhibit higher proton conductivities than a pristine sPEEK membrane and show more stable conductivities than Nafion®117 at a low humidity and high temperatures. For instance, the proton conductivity of Nafion®117 rapidly drop at a relative humidity of 40% and temperatures above 60°C, whereas the conductivity of the composite membranes increase up to 70°C, while maintaining similar values up to 80°C. The high water-absorption and water-retention capacities for the sPEEK/mesoporous material composite membranes are quantified in order to support the results for the different water uptake and proton conductivities.