The application of organic-inorganic nanocomposite membranes allows for a synergy between the desirable thermal and mechanical properties of inorganic materials with the reactivity, dielectric properties, durability, flexibility, and processability of the polymeric materials. Proton exchange membrane fuel cells (PEMFCs) suffer from some problems including water content management, carbon monoxide poisoning, hydrogen reformate, and fuel crossover through the membrane. Herein, specific solutions have been proposed to the above-mentioned problems using organ-inorganic nanocomposites. These solutions include doping proton conductive inorganic nano-particles in the proton exchange membrane, preparing nanocomposites via the sol-gel method, covalence bond of inorganic compounds with the polymer structure, and acid-based proton exchange nanocomposite membranes. Furthermore, hydrogen production with low carbon monoxide content using the ethanol steam reforming method, as well as the effect of CO in the hydrogen feed of PEMFC are explained and discussed. Finally, desirable conditions for achieving the maximum power density in exchange membrane cells (EMFCs) are discussed.