The principle of molecular recognition originating from the concept of lock-and-key has been one of the foundation stones for modern chemistry and biology. Molecular recognition in either biomolecules or synthetic molecules leads to non-covalent linkages, which are featured by responsiveness, reversibility and competition, differing from the covalent bonds. Therefore, recently, this concept has been introduced to and employed in the field of functional materials with great success. In this review, these materials will be examined from the molecular recognition point of view, without considering the origins of the binding pairs involved. First, the structural characters of hydrogels locked by molecular recognition are discussed in detail with emphasis on the chemical structure and architectures of the interaction pairs and the corresponding polymers. As the new hydrogel materials inherit the reversible advantages from non-covalent interactions as well as the specificities of the host–guest or ligand–acceptor pairs, their corresponding responses to various stimuli are discussed in the second part of this review. Compared to the smart materials made of responsive polymers, the hydrogels locked by molecular recognition are featured by the precise control of the responsiveness to various environmental stimuli via sophisticated design of the interaction sites by changing their chemical structures, density location and linking chemistry to the polymer backbones etc. Finally, representative applications of these hydrogels are briefly described.