As a novel class of three-dimensional (3D) hydrophilic cross-linked polymers, supramolecular hydrogels not only display unique physicochemical properties (e.g., water-retention ability, drug loading capacity, biodegradability and biocompatibility, biostability) as well as specific functionalities (e.g., optoelectronic properties, bioactivity, self-healing ability, shape memory ability), but also have the capability to undergo reversible gel-sol transition in response to various environmental stimuli inherent to the noncovalent cross-linkages, thereby showing great potential as promising biomaterial scaffolds for diagnosis and therapy. In this Review, we summarized the recent progress in the design and synthesis of supramolecular hydrogels through specific, directional noncovalent interactions, with particular emphasis on the structure-property relationship, as well as their wide-ranging applications in disease diagnosis and therapy including bioimaging, biodetection, therapeutic delivery, and tissue engineering. We believe that these current achievements in supramolecular hydrogels will greatly stimulate new ideas and inspire persistent efforts in this hot topic area in future.