Organs-on-chips composed of a porous membrane-separated, double-layered channels are used widely in elucidating the effects of cell co-culture and flow shear on biological functions. While the diversity of channel geometry and membrane permeability is applied, their quantitative correlation with flow features is still unclear. Immersed boundary methods (IBM) simulations and theoretical modelling were performed in this study. Numerical simulations showed that channel length, height and membrane permeability jointly regulated the flow features of flux, penetration velocity and wall shear stress (WSS). Increase of channel length, lower channel height or membrane permeability monotonically reduced the flow flux, velocity and WSS in upper channel before reaching a plateau. While the flow flux in lower channel monotonically increased with the increase of each factor, the WSS surprisingly exhibited a biphasic pattern with first increase and then decrease with increase of lower channel height. Moreover, the transition threshold of maximum WSS was sensitive to the channel length and membrane permeability. Theoretical modeling, integrating the transmembrane pressure difference and inlet flow flux with chip geometry and membrane permeability, was in good agreement with IBM simulations. These analyses provided theoretical bases for optimizing flow-specified chip design and evaluating flow microenvironments of in vivo tissue. Graphic