Among the different nanostructures that have been demonstrated as promising materials for various applications, three–dimensional (3D) nanostructures have attracted significant attention as building blocks for constructing high-performance nanodevices because of their unusual mechanical, electrical, thermal, optical, and magnetic properties arising from their novel size effects and abundant active catalytic/reactive sites due to the high specific surface area. Considerable research efforts have been devoted to designing, fabricating, and evaluating 3D nanostructures for applications, including structural composites, electronics, photonics, biomedical engineering, and energy. This review provides an overview of the nanofabrication strategies that have been developed to fabricate 3D functional architectures with exquisite control over their morphology at the nanoscale. The pros and cons of the typical synthetic methods and experimental protocols are reviewed and outlined. Future challenges of fabrication of 3D nanostructured materials are also discussed to further advance current nanoscience and nanotechnology.