In present Polymer Electrolyte Fuel Cell (PEFC), the cathode oxygen reduction reaction (ORR) is dominant at high current density condition. In order to accelerate this reaction, oxygen, proton and electron, which move in void space, ionomer and carbon black (CB) or CNT respectively, have to be transferred at Pt surface smoothly. Accordingly, it is very important to know the transport phenomena in catalyst layer (CL) to design the optimum structure and to develop new materials. In order to investigate the transport phenomena in CL by applying calculation technique, in this study, heterogeneous CB aggregate structure was simulated by computer calculation as the first examination. In addition, ionomer coating condition and proton conductivity were examined. Furthermore oxygen, proton and electron transfer in 3D porous catalyst layer were calculated, and the effective reaction field was examined in various structure and ionomer condition.