The catalyst layers (CLs) in proton exchange membrane fuel cells (PEMFCs) are porous composites of complex microstructures of the building blocks, i.e., Pt nano-particles, carbonaceous substrates and Nafion ionomers. It is important to understand the factors that control the microstructure formation in the fabrication process. A coarse-grained molecular dynamics (CG-MD) method is employed to investigate the fabrication process of CLs, which depends on the type and amount of components and also the type of the dispersion medium (ethylene glycol, isopropanol or hexanol) used during ink preparation of the catalyst-coated membranes (CCMs). The dynamical behaviors of all the components are outlined and analyzed following the fabrication steps. In addition, the Pt nano-particle size distribution is evaluated and compared with the labor testing. Furthermore, the primary pore size distributions in the final formations of three cases are shown and compared with the experiments. The sizes of the reconstructed agglomerates are also considered on the effect of solvent polarity. (C) 2012 The Electrochemical Society. [DOI: 10.1149/2.064203jes] All rights reserved.