The catalyst layer (CL) of a proton exchange membrane fuel cell involves various particles and pores that span a wide range of length scales, from several nanometers to a few microns. The success of the CL design depends decisively on understanding the detailed structure in microscale or even in nanoscale. In this paper, the properties of nano-/microstructures are outlined, and the physical and chemical processes are analyzed on the Pt surfaces. A software package of automatic simulation environment is developed and applied to investigate the electronic structure of the Pt–H system. Then, the dissociative adsorption process is obtained using the nudged elastic band approach. The modeling of the nanocomposites in the CLs is a multiscale problem. The nanoscale models are used for investigating the structural evolution and the interactions between Pt/C particles and polymer components; while the microscale simulations, which aim to bridge molecular methods and continuum methods, are extended to describe the morphology of heterogeneous materials and rationalize their effective properties beyond length- and time-scale limitations of the atomistic simulations. However, there are still some major challenges and limitations in these modeling and simulations. The multiscale modeling should be developed to demonstrate the usefulness for engineering design with the longstanding goal of predicting particle-structure-property.