This work successfully developed a multi-objective optimization approach for enhanced microstructure of the gas diffusion layer. A design of virtual experiments approach was initially utilized to achieve a uniform distribution of sample points within the defined parameter space. This space encompassed key GDL manufacturing parameters such as fiber diameter, fiber concentration, binder concentration, GDL thickness, and compression ratio. The maximum and minimum values of the input range properties were defined to be in good agreement with previous literature reports. Subsequently, these sample points were used as input parameters to stochastically generate GDL microstructures. From these generated microstructures, essential output properties were digitally characterized through physics-based calculations, such as thermal and electrical conductivities, diffusivity, and contact resistance between the GDL and the MPL.