Well-developed pore channels and large effective permeation area are sorely needed in developing highly permeable synthetic membranes for the reduction of energy consumption in separation processes. Herein, water stable, soluble and reactive amino-functionalized metal-organic polyhedron (MOP) ZrT-1-NH with intrinsic porosity is co-assembled with lysine (Lys) into a new kind of thin-film nanocomposite (TFN) membranes through in situ interfacial polymerization (IP) with trimesoyl chloride (TMC). Striped structure on the membrane surface is induced by the participation of the amino-MOP in polymerization, which greatly enhances the effective permeation area of the separation layer compared with the membranes feature smooth surface. Meanwhile, the suitable pore aperture of the introduced ZrT-1-NH can also benefit the diffusion of water molecules and block the transport of molecules with bulkier molecular volumes. The results showed that the formed membrane exhibits significantly improved water permeance (27.3 L m h bar, 480% increase) compared with that of the pristine Lys/TMC membrane (4.7 L m h bar). The compositing of ZrT-1-NH also leads to an increase in the rejection selectivity of dye and salt, rejection selectivity of dye/salt mixture, as well as in antifouling and antibacterial properties, making the ZrT-1-NH-Lys/TMC composite membrane a potential choice for dye/salt separation. Moreover, this work demonstrates the bright prospects of applying soluble and reactive porous cages in the development of high-loading defect-less TFN membranes for efficient molecular separations.