Current in vitro gut models lack physiological relevance, and various approaches have been taken to improve current cell culture models. For example, mimicking the three-dimensional (3D) tissue structure or fluidic environment has been shown to improve the physiological function of gut cells. Here, we incorporated a collagen scaffold that mimics the human intestinal villi into a microfluidic device, thus providing cells with both 3D tissue structure and fluidic shear. We hypothesized that the combined effect of 3D structure and fluidic shear may provide cells with adequate stimulus to induce further differentiation and improve physiological relevance. The physiological function of our ‘3D gut chip’ was assessed by measuring the absorptive permeability of the gut epithelium and activity of representative enzymes, as well as morphological evaluation. Our results suggest that the combination of fluidic stimulus and 3D structure induces further improvement in gut functions. Our work provides insight into the effect of different tissue environment on gut cells.