Nanoparticles of 2D hexagonal mesoporous SBA-15 silica were prepared for the first time and mixed in Nafion to form composite membranes by solvent casting method. The SBA-15 nanoparticles containing P123 surfactant (S-SBA-15n) and that extracted with ethanol (Ex-SBA-15n) were used as the inorganic fillers in order to see the effect of pore-directing agent on the performance of resultant composite membranes. The physico-chemical properties of SBA-15 nanoparticles were examined with powder XRD, N-2 sorption, TGA and SEM. The methanol permeability, proton conductivity, and cell performance of the resultant composite membranes were compared in terms of the content of SBA-15 nanoparticles and whether the pore-directing agent was removed. The optimal proton conductivities were obtained for the composite membranes with 5 wt% loading of SBA-15 nano-particles. Moreover, the P123 pore-directing agent present inside the pores of S-SBA 15n was found to effectively resist methanol permeation from anode to cathode and also assist the proton transferring. The single cell assembled with 5 wt% S-SBA-15n/Nafion composite membrane gave the highest power density of 117 mW cm(-2) at 60 degrees C, which was about 80% higher than the cell with recast Nafion membrane and also 23% higher than that with commercial membrane of Nafion (R) 117.