The FAS(Fluoroalkylsilane)/Nafion inorganic-organic composite electrolyte membrane was successfully fabricated through sol-gel method. The FAS having hydrophobic functional group and silanol ligands is impregnated in $Nafion^{(R)}$ membrane to reduce methanol crossover. The prepared FAS/Nafion inorganic-organic composite electrolyte membrane consist of the hydrophobic FAS-derived silicate nano-particles and $Nafion^{(R)}$ matrix showed decrease of methanol crossover and reduction of humidity dependence without large sacrifice of proton conductivity. The microstructural analysis of the composite membranes was performed using FESEM and FTIR. And the effect of the incorporation of the hydrophobic FAS-derived silicate nano-particles into $Nafion^{(R)}$ membrane was investigated via solvent uptake, membrane expansion rate, humidity dependency of proton conductivity and contact angle measurement.