In this paper, we analyzed the nanoscale transport phenomena in membrane electrode assembly (MEA) of polymer electrolyte fuel cell (PEFC) by large scale molecular dynamics (MD) simulations. Especially, (1) transport phenomena of proton and water in polymer electrolyte membrane (PEM), (2) oxygen permeability of ionomer in catalyst layer (CL), and (3) transport phenomena of water droplet in a nano pore were simulated, and the nanoscale transport characteristics were analyzed in detail. In the analysis of proton transfer in PEM, the simulation results were compared with some experimental results to evaluate the validity of our simulation. With regards to the oxygen permeability of ionomer, the dependence of water content on the permeability was estimated and the difference of characteristics between ionomer and bulk membrane was discussed. In the analysis of transport phenomena of a water droplet in a nano pore, we compared the results of our simulation with macroscopic governing equation.