Toward rational design of polymer electrolyte fuel cell (PEFC), understandings of both atomistic scale and systems characteristics are important. Multi-scale simulation can contribute to bridging microscopic and macroscopic understandings effectively. In this manuscript, we described a multi-scale simulation approach based on an original porous structure simulator and computational chemistry methods. Proton conductivity was estimated by molecular dynamics method and structures of porous catalyst layer were modeled by the porous structure simulator. Multi-scale simulations for macroscopic current-voltage characteristics of PEFC were performed considering both atomistic-scale properties and porous microstructure. Influences of atomistic properties and microstructure of porous catalyst layer on macroscopic currentvoltage characteristics were successfully studied. Effectiveness of the developed multi-scale simulation approach was confirmed from the simulation results.