Atomic scale characterization and manipulation is one of the physical bottlenecks, which needs to be broken when realizing atom manufacturing. The aberration-corrected transmission electron microscopy (TEM) is a powerful tool for structural characterization due to its exceptional spatial resolution. Therefore, it is very crucial to co-characterize atomic-scale three-dimensional structure and properties of atomic manufacturing materials by using TEM, which allows us to further understand the physics mechanism of atomic manipulation of materials. Nano-clusters and nanoparticles are two of the main objects in the studies of atomic manufacturing materials and devices, and possess rich physical and chemical properties and high manoeuverability. In this paper, we summarize the recent progress of quantitatively determining three-dimensional structures and magnetic properties of nanocluster, nanoparticles and nanograins, as well as their dynamic evolutions under the working conditions. The methodological breakthrough and development of electron microscopy techniques provide a solid foundation for precisely controlling atomic manufacturing materials.