Dynamic gut-on-a-chip platform allows better recreation of the intestinal environment in vitro compared to the traditional static cell culture. However, the underlying mechanism is still not fully discovered. In this study, the shear stress behavior in a gut-on-a-chip device with porous membrane subjected to peristalsis motion is numerically investigated using CFD simulation for three different pore sizes and two pattern layouts. The results reveal that, in the stationary microchannel, the average shear stress on the porous membrane is approximately 15% greater than that of the flat membrane, regardless of the pore size. However, when subjected to cyclic deformation, the porous membrane with smaller pore size experiences stronger variation of shear stress which is ±5.61%, ±10.12% and ±34.45% from its average for the pore diameters of 10 μm, 5 μm and 1 μm, respectively. The shear stress distribution is more consistent in case of the staggered pattern layout while the in-line pattern layout allows for a 32% wider range of shear stress at the identical pore size during a cyclic deformation. These changes in the shear stress caused by peristalsis motion, porous size and membrane pattern could be the key factors that promote cell differentiation in the deforming gut-on-a-chip model.