Covalent organic cages (COCs), distinguished by their discrete, three-dimensional architectures with customizable cavities, represent a rapidly advancing class of molecular materials with broad applications, including microreactors, heterogeneous catalysis, high-permeability membranes, and porous liquids. Recent advancements in synthetic strategies and supramolecular chemistry have enabled a diverse range of COC structures, which, like metal-organic frameworks (MOFs), covalent organic frameworks (COFs), and porous organic polymers (POPs), provide high surface areas, accessible porosities, and tunable architectures. Unlike these extended porous networks, COCs are composed of discrete, solvent-soluble units, facilitating enhanced dispersion, processability, and recyclability. Their dynamic features, including reversible polymorphism and supramolecular interactions, support dissociation and recombination, further enhancing their adaptability and shape persistence. This review examines recent progress in the use of COCs for supramolecular separations, with a focus on their utility in separating gases, ions, enantiomers, and positional isomers, as well as in the development of pure and hybrid porous membranes. By synthesizing current findings, we aim to assist researchers in designing COCs tailored to specific industrial separation applications, highlighting the increasing relevance of these materials in separation science.