Porous membranes separate two microfluidic channels comprising organ-on-a-chip systems, enabling interaction between cells cultured in both channels. Although it is evident that the material and structural characteristics of porous membranes affect the microfluidic environment in organ-on-a-chip systems, porous membranes have not been studied extensively. Here, we examine the influence of structural parameters of porous membranes on the microenvironment within an organ-on-a-chip system using computational fluid dynamics. Our findings highlight the necessity of a comprehensive consideration of pore diameter and pore density to design an optimal porous membrane that simultaneously enhances solute permeability and deformation. This research suggests the potential for a more accurate design of physiological conditions in organ-on-a-chip systems by precisely adjusting the structural parameters of porous membranes.