Modifying nanostructures of colloidal quantum dots (QDs), such as forming core/shell structures and alloying, is a common strategy for tuning their optical properties. However, the relationship between the actual nanostructures and optical properties of QDs remains poorly discussed owing to inherent difficulties in the structural analysis of QDs. Here, we investigated nanostructures of CuInSe2/ZnS core/shell QDs as a function of temperature during ZnS shell growth using X-ray energy-dispersive spectroscopy spectrum imaging combined with multivariate statistical analysis. Lower signal-to-noise ratios resulting from very weak characteristic X-rays emitted from QDs were overcome using an aberration-corrected transmission electron microscope equipped with a large solid-angle X-ray detection system (total solid angle of 1.6 sr). The nanoscale X-ray mapping elucidated that QDs with homogeneous cores and island-like shells surrounding core vertexes were formed at temperatures of 225 and 250 °C. Moreover, diffusion of Zn atoms from shells to cores was revealed by quantitative analysis of the core composition and verified by atomic diffusion simulations. These modified nanostructures should contribute to the decrease in surface traps and internal defects, enhancing the optical properties of QDs. The nanoscale X-ray mapping provides direct evidence of modified nanostructures of QDs.