Fabrication of hybrid membranes composed of porous materials embedded in polymer matrices is a subject of topical interest. Herein, we introduce a new class of hybrid membranes: hyper-cross-linked metal-organic polyhedra (HCMOPs). These membranes are based upon soluble MOPs that can serve as high-connectivity nodes in hyper-cross-linked polymer networks. HCMOPs spontaneously form macro-scale, defect-free, freestanding membranes, and, thanks to the covalent cross-linking of MOPs, the resulting membranes possess multiple functionalities: strong water permeability; self-healing ability; antimicrobial activity; and better separation and mechanical performance than pristine polyimine membranes. This study introduces a new concept for the design and fabrication of multifunctional membranes and also broadens the applications of MOPs.