Chiral molecular cages are demonstrated to have unique applications in enantioselective chemistry owing to their 3D cage-like geometry and intrinsic cavity. Yet, the role of the chirality of molecular cages in their physical properties of condensed materials, for example, the manipulation of electronic spin behaviors, remains elusive. Here, we report that chiral organic molecular cages can become an appealing chiral system to realize highly efficient spin filtering through the chirality-induced spin selectivity (CISS) effect. A pair of triphenylphosphine-containing organic cages (Pcages) with opposite handedness can manifest a very high spin polarization of nearly 90% and a high conductivity that exceeds those of other chiral molecules and structures by 2 orders of magnitude. By fabricating such molecular cages into thin-film spin filter devices, they have outstanding magnetoresistance ratios up to 12% among most of the devices based on the CISS effect. More interestingly, the Pcages can self-assemble with triphenylborane molecules through B-P frustrated Lewis acid-base complexation to form homochiral helical supramolecular nanofibrils. The spin-selective transport capacity and magnetic resistance obtained unexpected enhancement within these cage-based assemblies. This study demonstrates the potential of organic cages as a new chiral platform for controlling spin selectivity and will inspire the creation of new spintronic devices using chiral organic cage materials.