The structural analysis serves as a bridge to link the structure of materials to their properties. Revealing the structure details allows a better understanding on the growth mechanisms and properties of materials, and a further designed synthesis of functional materials. The widely used methods based on X-ray diffraction have certain limitations for the structural analysis when crystals are small, poorly crystallized or contain many defects. As electrons interact strongly with matter and can be focused by electromagnetic lenses to form an image, electron crystallography (EC) approaches become prime candidates for the structural analysis of a wide range of materials that cannot be done using X-rays, particularly nanomaterials with poor crystallinity. Three-dimensional electron diffraction tomography (3D EDT) is a recently developed method to automatically collect 3D electron diffraction data. By combining mechanical specimen tilt and electronic e-beam tilt, a large volume of reciprocal space can be swept at a fine step size to ensure the completeness and accuracy of the diffraction data with respect to both position and intensity. Effects of the dynamical scattering are enormously reduced as most of the patterns are collected at conditions off the zone axes. In this thesis, 3D EDT has been used for unit cell determination (COF-505), phase identifications and structure solutions (ZnO, Ba-Ta3N5, Zn-Sc, and V4O9), and the study of layer stacking faults (ETS-10 and SAPO-34 nanosheets). High-resolution transmission electron microscope (HRTEM) imaging shows its particular advantages over diffraction by allowing observations of crystal structure projections and the 3D potential map reconstruction. HRTEM imaging has been used to visualize fine structures of different materials (hierarchical zeolites, ETS-10, and SAPO-34). Reconstructed 3D potential maps have been used to locate the positions of metal ions in a woven framework (COF-505) and elucidate the pore shape and connectivity in a silica mesoporous crystal. The last part of this thesis explores the combination with X-ray crystallography to obtain more structure details.