Tissues and organs possess an organized cellular arrangement that enables their unique functions. However, conventional three-dimensional (3D) encapsulation techniques fail to recapitulate this complexity due to the cell migration during cell culture. In biological tissues, basement membranes (BMs) are essential to mechanically support cellular organization. This study finds that a positively charged outermost surface of multilayered nanofilms, fabricated through layer-by-layer assembly of poly-l-lysine (PLL) and dextran (Dex) via hydrogen bonds, stimulates the barrier functions of BMs. This type of artificial BM (A-BM) demonstrates enhanced barrier properties in comparison to other types of A-BMs composed of BM components such as collagen type IV and laminin. Such an enhancement is potentially associated with the outermost cationic layer, which inhibits the sprouting of endothelial cells (ECs) and effectively prevents EC migration over a 14-d period, aligning with the formation timeline of natural BMs in 3D tissues. Finally, 3D organized vascular channels are successfully engineered with the support of shape-adaptable PLL/Dex nanofilms. This approach offers a guideline for engineering organized 3D tissue models by regulating cell migration, which can provide reliable platforms for in vitro permeability assay of new drugs or drug delivery carriers.