This study examines the impact of ionomer to carbon mass ratio and the number of platinum particle clusters on the structural dynamics and organization of Pt-C-Nafion catalyst layers during the evaporation process. Using Coarse-Grained Molecular Dynamics (CGMD) simulations, we analyzed the center of mass position and ionomer coverage on Pt surface. The results show that a higher ionic polymer to carbon mass ratio (0.6) increases lateral mobility and short-range ordering along with the coverage of the Pt surface with ionomers, whereas increasing the number of Pt particle clusters (from 1 to 4 ) enhances lateral diffusion as well as leading to more difficult adsorption of ionomers. These findings highlight the importance of optimizing these parameters to obtain a homogeneous and stable catalyst layer, which is critical for fuel cell performance. Future work will include tuning the Pt/C mass ratio, hydrophilicity, and IC ratio in conjunction with energy and force analyses to further understand the effect of Nafion on Pt/C clusters.