In the thesis, TEM has successfully been applied leading to a better understanding of the Ⅲ-nitride material system and devices. We successfully deposit GaN layers and InGaN/GaN multiple quantum wells(MQWs) on sapphire by metalorganic chemical vapor deposition(MOCVD) and pulsed laser deposition(PLD). There are many stacking faults and mismatch dislocations exiting near the interface to release the strain originated from lattice mismatch between sapphire and epitaxial layers. These samples have high defects density. We also successfully deposit GaN layers on Si substrate and ZnO substrate. Although they are promising substrate, there are still many problems need to be addressed. The large thermal expansion and lattice mismatch between Si-substrate and epilayers cause cracks on the growth surface and lead to high defects density. Poor surface preparation and severe issues associated with high temperature growth by MOCVD degrade the GaN film quality on ZnO substrate. In chapter 4-3, Multiple In0.18Ga0.82N/GaN MOWs layers in a green LED were observed by high-angle annular dark-field scanning transmission electron microscope (HAADF-STEM) and high resolution TEM (HRTEM). HAADF-STEM provided undoubted evidence that V defects in the multiple QWs have the thin six-walled structure with InGaN/GaN {10 1} layers. The detailed structure of the observed V defects is discussed on the basis of the formation mechanism of V defects which was proposed taking into account the growth kinetics of the GaN crystal and a masking effect of In atoms segregated around the threading dislocation. In chapter 4-4, we investigated the nanostructure of AlGaN/GaN strained-layer superlattice (SLS) cladding in the GaN-based violet LD and the AlInGaN-based ultraviolet (UV) LED with a STEM. In the p-SLS cladding, comprising thirty four pairs of p-Al0.1Ga0.9N/p-GaN:Mg layers in the GaN-based LD, the Al0.1Ga0.9N and GaN layers were distinguished as dark and bright bands ~6 nm wide in the HAADF-STEM images. Threading dislocations (TDs) were observed. Among of TDs that came from the underlying layer, some run outside through the SLS, and the others disappeared within the SLS, which discloses a role of the SLS in suppressing defect propagation. A HAADF-STEM image of the TD with a dark line along the center of a bright contour was found. One of probable explanations for the dark line is local segregation of light atoms (Mg or Al) in Cottrell atmosphere around the dislocation core. In the HAADF-STEM image of the UV LED wafer, the AlInGaN and AlInGaN:Si layers in the MQW were definitely resolved, appearing as dark and bright bands. HAADF-STEM also distinguished between the AlGaN and GaN layers in the p-SLS cladding in the UV LED wafer. In the last chapter, high density InGaN quantum dots (QDs), grown on the GaN underlying layer which was partially masked with SiNx nano-crystals, were investigated by HAADF-STEM, HRTEM and energy dispersive X-ray spectroscopy. The layer of SiNx masks appeared as a dark line in HAADF-STEM images and the height of the masks was roughly estimated to be less than 2 nm from the thickness of the dark line. The InGaN QDs were observed as bright triangles in the HAADF-STEM images. The QDs can be regarded as nano island crystals with the {10 1} side walls and a height of several nanometers. The lattices in the InGaN crystals were strained compared with the underlying and the capping GaN lattices, contacting in the coherent lattice relation with them.