Charged Au nanoparticles with various diameters, from 2.7 nm to 10.3 nm, were synthesized by using various reducing agents. Then charged Au nanoparticles were self-assembled onto the NafionTM membrane surface as methanol barriers. It was found that the proton exchange membrane self-assembled with 3.9 nm Au particles had the lowest methanol crossover. The proton conductivity decreased with the increase of the particles size until the particles size was more than 6.2 nm and they had little influence on the membrane conductivity. All the self-assembled membranes have higher open circuit voltage (OCV) and performance than original Nafion212TM membrane. And the membranes self-assembled with 3.9 nm poly (diallymethylammonium chloride) (PDDA) modified Au (PDDA-Au) particles had the highest performance due to the reciprocal of the methanol permeation current density and membrane area resistance.