Three-dimensional (3D) nanostructures have attracted widespread attention in physics, chemistry, engineering sciences, and biology devices due to excellent functionalities which planar nanostructures cannot achieve. However, the fabrication of 3D nanostructures is still challenging at present. Reliable fabrication, improved controllability, and multifunction integration are desired for further applications in commercial devices. In this review, a powerful fabrication method to realize 3D nanostructures is introduced and reviewed thoroughly, which is based on atomic layer deposition assisted 3D assembly through various sacrificial templates. The aim of this review is to provide a comprehensive overview of 3D nanofabrication based on atomic layer assembly (ALA) in multifarious sacrificial templates for 3D nanostructures and to present recent advancements, with the ultimate aim to further unlock more potential of this method for nanodevice applications.