The present invention relates to a proton conductive nanocomposite membrane comprising a fluorinated proton conductive polymer substance introduced with polyhedral oligomeric silsesquioxane (POSS) having a proton donor and polyhedral oligomeric silsesquioxane (POSS) having a proton acceptor, and a method for preparing the same, in which the addition of the very small size POSS having proton donors and POSS having proton acceptors to the nanocomposite membrane increases ion conductivity due to easy hopping of generated protons (cations) within ion channels, thereby realizing excellent proton conductivity while the nanocomposite membrane shows excellent mechanical strength even though the degree of sulfonation of the membrane is increased.