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Two different types of silica oxide were prepared as filler in sulfonated polymers for fuel cell applications operated under water deficient environment. SiO2 nanoparticle and thiol-embedded SiO2 nanoparticles were mechanically mixed with sulfonated (arylene ether sulfone) solutions, and then the mixtures were cast to prepare composite membranes. The composite membranes with different amount of SiO2 were prepared to investigate the effect of two types of SiO2 nanoparticles on ionic conductivity with relative humidity at 120 oC. In addition, ion exchange capacity,water uptake, thermogravitational analysis, differential scanning calorimetry were studied. As results, the composite membranes containing thiol-embedded SiO2 showed better water-channel forming ability at low relative humidity less than 50% in this study. Under full hydration of the composite membranes, the composite membranes containing pure SiO2 nano-particles have higher ionic conductivity since the thiol-embedded SiO2 might cause steric hindrance to make water channel well connected. Thus, below 50% relative humidity, the composite membranes containing 10 wt% of thiol-embedded SiO2 showed the best ionic conductivity. It is very promising for polymer electrolyte fuel cells operated normally under 50% relative humidity at cathode.