Mesoporous SBA-15 nanoparticles were prepared for the first time. SBA-15 nanoparticles were loaded into Nafion to form composite membranes. Comparison was made on composite membranes containing as-made or extracted SBA-15. Pore-directing agent assisted proton conductivity and resisted methanol permeability. MEA assembled with composite membrane containing as-made SBA-15 gave 80% higher power density than that with plain Nafion.