Here, we report a multiplex culture system that enables simultaneous recreation of multiple replications of the three-dimensional (3D) microarchitecture of the human intestinal epithelium in vitro. The "basolateral convective flow-generating multi-well insert platform (BASIN)" contains 24 nano-porous inserts and an open basolateral chamber applying controllable convective flow in the basolateral compartment that recreates a biomimetic morphogen gradient using a conventional orbital shaker. The mechanistic approach by which the removal of morphogen inhibitors in the basolateral medium can induce intestinal morphogenesis was applied to manipulate the basolateral convective flow in space and time. In a multiplex BASIN, we successfully regenerated a 3D villi-like intestinal microstructure using the Caco-2 human intestinal epithelium that presents high barrier function with minimal insert-to-insert variations. The enhanced cytodifferentiation and proliferation of the 3D epithelial layers formed in the BASIN were visualized with markers of absorptive (villin) and proliferative cells (Ki67). The paracellular transport and efflux profiles of the microengineered 3D epithelial layers in the BASIN confirmed its reproducibility, robustness, and scalability for multiplex biochemical or pharmaceutical studies. Finally, the BASIN was used to investigate the effects of dextran sodium sulfate on the intestinal epithelial barrier and morphology to validate its practical applicability for investigating the effects of external chemicals on the intestinal epithelium and constructing a leaky-gut model. We envision that the BASIN may provide an improved multiplex, scalable, and physiological intestinal epithelial model that is readily accessible to researchers in both basic and applied sciences.