Graphdiyne (GDY) is a 2D carbon allotrope that features a one-atom-thick network of sp- and sp2-hybridized carbon atoms with high degrees of π conjugation. Due to its distinct electronic, chemical, mechanical, and magnetic properties, GDY has attracted great attention and shown great potential in various fields, such as catalysis, energy storage, and the environment. Preparation of GDY with various nanostructures, including 0D quantum dots, 1D nanotubes/nanowires/nanoribbons, 2D nanosheets/nanowalls/ordered stripe arrays, and 3D nanospheres, greatly improves its function and has propelled its applications forward. High biocompatibility and stability make GDY a promising candidate for biomedical applications. This review introduces the latest developments in fabrication of GDY-based nanomaterials with various morphologies and summarizes their propective use in the biomedical domain, specifically focusing on their potential advantages and applications for biosensing, cancer diagnosis and therapy, radiation protection, and tissue engineering.