CdSe/ZnS core–shell structured nano-crystal quantum dots (QDs) are ideal candidates for light-emission applications due to their high quantum efficiency, narrow-band, and particle-size-tunable photoluminescence. In particular, their small size results in the quantum confinement of semiconductor nano-crystals, which widens their energy gaps. In general, structural analyses of QDs using a transmission electron microscope (TEM) are very important due to the significantly small size of QDs. We were able to obtain structural information of CdSe/ZnS core–shell QDs using nano-beam diffraction by controlling the nano-probe of the dark field scanning TEM (DF-STEM) mode and strain analysis with high-resolution TEM (HRTEM)/STEM images. Furthermore, we could clearly distinguish the interface between the CdSe core and the ZnS shell from the strain analysis with the HRTEM/STEM images.