Graphdiyne (GDY) is a carbon allotrope that has attracted great attention since it was first synthesized in 2010. The sp-hybridized carbon atoms give GDY many fascinating properties. In recent years, GDY-based nanostructures have been proved to demonstrate significant advantages in various fields through experiments and theoretical calculations. With the aim of comprehensively introducing the configuration of GDY-based nanostructures at the microscopic level, this review begins from the structure of GDY, followed by introducing the compound structures of GDY with atoms, molecules, ions, and nanoparticles. Recent progress and achievements on the syntheses of GDY and GDY-based nanostructures are overviewed. Subsequently, the application of GDY-based nanostructures in catalysis, energy storage, and biology are summarized. Finally, the current development status of GDY-based nanostructures is summarized, and the future development direction is prospected.