Ion permeability characteristics in nano-polymer membrane structures are performed to investigate the chemical composition and characteristics of MEA(Membrane Electrolyte Assembly) which is one of the most important parts to decide the performance in PEMFC(Polymer Electrolyte Membrane Fuel Cell) system. Subsequently, the MEA manufacturing process is presented for the uniformed MEA product. In the meantime, the analysis of SEM(Scanning Electron Microscope) is carried out in order to investigate the joint aspect and chemical composition of MEA. As a result of SEM analysis, it is found that the bonded catalyst and carbon composition contain the reasonable amount to get unit cell output. It is also found that the humidification gives the better performance result slightly.