The 3D atomic arrangements of materials determine the free energy landscape, thus governing the physical and catalytic properties of those materials. The 3D structures of nanoparticles can deviate from the periodic atomic arrangement of their bulk counterparts due to the dominance of surface dangling bonds, defects, and dislocations. One approach to understand the structure of nanoparticles and their resulting unique properties involves precise probing of the 3D positions of all constituent atoms of individual nanoparticles. The 3D electron tomography and Brownian one particle reconstruction allow investigation of the 3D atomic positions of nanoparticles. Both methods use transmission electron microscopy (TEM) or scanning TEM (STEM) images of nanoparticles with different projection angles and collect their phase information in reciprocal space to reconstruct the 3D structure of the particles. The thus-reconstructed 3D maps of metal nanoparticles are highly resolved, facilitating the determination of their atomic coordinates. Grain boundary, dislocation, and lattice expansion are observed on the 3D atomic maps. On the basis of the 3D atomic maps, the physical properties of individual nanoparticles can be accurately predicted, enabling purpose-driven synthesis.