Coarse-grained molecular dynamics simulations were performed to understand the evolution of ionomer morphologies in solutions during solvent evaporation. To reproduce experimental fabrication conditions, the simulation conditions, such as evaporation and sedimentation rate, were determined based on a dimensionless parameter, the Peclet number, providing a direct link between simulation results and experimental findings. The effects of ionomer loading and substrate wettability on the morphologies of ionomer thin films after drying were investigated extensively, which exhibit similar trends reported in experiments. At low ionomer loading, a discontinuous patchy film with a minimum thickness of approximate to 3 nm was formed on the hydrophobic substrate, whereas a high-coverage continuous film of approximate to 2 nm thickness was found on the hydrophilic substrate. At high ionomer loading, regardless of the substrate wettability, a lamellar-like morphology with multiple water-rich layers was observed, although the stability of the layer structures and the ionomer surface roughness differ between the substrate types because the substrate wettability strongly affects the adsorption behaviors of ionomers and water as the first layer in the interfacial region. Our findings of a decrease in the degree of phase segregation with increasing thickness suggest an eventual collapse of the lamellar structure at a certain thickness within a few tens of nanometers or even thinner.