This work is comprised of a versatile multiscale modeling of carbon corrosion processes in catalyst layers (CLs) of polymer electrolyte fuel cells (PEFCs). Slow rates of electrocatalytic processes in CLs and materials aging are the main sources of voltage loss in PEFCs under realistic operating conditions. We combined microstructure data obtained from coarse-grained molecular dynamics (CGMD) simulations with a detailed description of the nanoscale elementary kinetic processes and electrochemical double-layer effects at the catalyst/electrolyte and carbon/electrolyte interfaces. We exclusively focused on morphology and microstructure changes in the catalyst layer of PEFCs as a result of carbon corrosion. By employing extensive CGMD simulations, we analyzed the microstructure of CLs as a function of carbon loss and in view of ionomer and water morphology, water and ionomer coverage, and overall changes in carbon surface. These ingredients are integrated into a kinetic model, which allows capture of the impact of the structural changes on the PEFC performance decay. In principle, such multiscale simulation studies allow a relation of the aging of CLs to the selection of carbon particles (sizes and wettability), the catalyst loading, and the level of ionomer structural changes during the CL degradation process.