ABSTRACT Molecular recognition is a crucial process in multiple areas, including separation, storage, and catalysis etc. Covalent organic cages (COCs), owing to their preorganized 3D cavities, customizable binding sites, and outstanding chemical stability, have been widely used for molecular recognition. Among the components of COCs, the covalent linkers play a crucial role in molecular recognition by shaping cavities and providing noncovalent interactions. In this concept, we exemplified recent progress in COC‐based host‐guest recognition, briefly summarized the bonding strategies (both dynamic and irreversible) used in covalent linkers for COC construction, and discussed how these linkers influence guest encapsulation by adjusting size, shape, and binding sites of their cavities. These insights are expected to provide a reference for the design of novel COCs for molecular recognition.