Energy-dispersive X-ray spectroscopy (EDX) is often performed simultaneously with high-angle annular dark-field scanning transmission electron microscopy (STEM) for nanoscale physico-chemical analysis. However, high-quality STEM-EDX tomographic imaging is still challenging due to fundamental limitations such as sample degradation with prolonged scan time and the low probability of X-ray generation. To address this, we propose an unsupervised deep learning method for high-quality 3D EDX tomography of core–shell nanocrystals, which can be usually permanently dammaged by prolonged electron beam. The proposed deep learning STEM-EDX tomography method was used to accurately reconstruct Au nanoparticles and InP/ZnSe/ZnS core–shell quantum dots, used in commercial display devices. Furthermore, the shape and thickness uniformity of the reconstructed ZnSe/ZnS shell closely correlates with optical properties of the quantum dots, such as quantum efficiency and chemical stability.