While tissue morphological processes take place mostly during ontogeny, the biliary duct in the liver can remodel itself even in adulthood. Due to the liver trait being susceptible to various injuries, the biliary duct changes its morphology to adapt to the types of injuries. Despite its functional importance for liver regeneration, the mechanisms regulating this biliary remodeling, especially those specific to types of injuries, remain unknown. Previously, our group revealed that Klf5, a biliary transcription factor, promotes the biliary cell proliferation under cholestasis, a type of liver injury, and thereby regulates biliary remodeling, using the Klf5 liver-epithelial-specific knockout mice (H. Okada et al., JBC, 2018). Besides the defect in biliary cell proliferation in these mutant mice, we observed isolated biliary cell clusters from the biliary duct, which cannot be explained by the cell proliferation defect, implying another function of Klf5 in structural maintenance. In this study, we developed a novel optimal culture system to represent 3D biliary structures in vitro, which enables us to observe the biliary morphology at the time-lapse live imaging. Combined with gene editing technology, we identified genes commonly affected by the loss of Klf5 both in vitro and in vivo. We found that Klf5 regulates the epithelial integrity during the remodeling and the extracellular matrix, including Lamb3, which encodes a component of laminin-332. Furthermore, we demonstrated the involvement of Lamb3 in the epithelial integrity by the Lamb3 liver-epithelial specific knockout mice. Our study shed light on an adult epithelial integrity mechanism while undergoing remodeling.