Molecular nanomaterials built with well-defined chemical structures, accurate molecular weights and high synthetic reproducibility, have emerged as an exciting new branch of nanomaterials. Meaningfully, they perfectly fill the gap between small molecules and conventional nanomaterials. Nevertheless, coordination-based molecular nanomaterials are especially attractive due to their diverse structures and multifunctionalities combining merits of both organic components and metal ions. This review highlights recent progresses of coordination-based molecular nanomaterials mainly involving biomedically relevant applications, such as biosensing, bioimaging and therapy. Three typical coordination-based molecular nanomaterials were emphasized: (1) Organometallic carborane nanoclusters showed high amount of boron, as well as varieties of optical properties by the incorporation between metals/metal complexes and carborane, make a great contribution to bioimaging and boron neutron capture therapy. (2) Atomically precise metal nanoclusters cascading metals as a whole, thus possessing intriguing structures and diverse optical properties, which are superior in biosensing, bioimaging and phototherapy. (3) Metal-organic nanocages assembled as containers play an important role in biosensing and biomolecular delivery because of host–guest interactions, and they also display excellent DNA binding for antitumor. Finally, the current challenges and perspectives for the further trend are also discussed. The overview will lead timely recognition of coordination-based molecular nanomaterials and hopefully stimulate their fast development.