Abstract CdSe@CdS Core@shell quantum dots (QDs) have been widely studied in recent years, due to their architecture which allows to tailor properties by controlling structure and composition. However, since CdSe and CdS have the same crystal structure, same cations, and similar lattice parameters, it is very challenging to image the interface. Herein, high‐resolution transmission electron microscopy, high‐angle annular dark‐field imaging, and energy‐dispersive X‐ray spectroscopy elemental mapping are combined to characterize the core@shell structure and identify the interface in the CdSe@CdS QDs with different CdS shell thicknesses. By examining changes in lattice spacing in an individual CdSe@CdS quantum dot, the atomic core@shell interface is identified. For thin‐shelled QDs, an ideal coherent interface forms between core and shell due to the small lattice mismatch, and the lattice spacing remains unchanged at the core and shell regions. For thick‐shelled QDs, the lattice spacing is different at the core and shell regions, while the heterostructured interface is still coherent and cannot be clearly imaged. As the shell thickness further increases, a sharp core@shell interface appears. The results define an approach to characterize the heterostructure of two materials with the same crystalline structure and cations.