The physical and chemical properties of nanophase materials rely on their crystal and surface structures. Transmission electron microscopy (TEM) is a powerful and unique technique for structure characterization. The most important application of TEM is the atomic-resolution real-space imaging of nanoparticles. This article introduces the fundamentals of TEM and its applications in structural determination of shape-controlled nanocrystals and their assemblies. By forming a nanometer size electron probe, TEM is unique in identifying and quantifying the chemical and electronic structure of individual nanocrystals. Electron energy-loss spectroscopy analysis of the solid-state effects and mapping the valence states art: even more attractive. In situ TEM is demonstrated for characterizing and measuring the thermodynamic, electric, and mechanical properties of individual nanostructures, from which the structure-property relationship can be registered with a specific nanoparticle/structure.