Self-assembled quantum dots (QDs) are potential candidates for photoelectric and photovoltaic devices, because of their discrete energy levels. The characterization of QDs at the atomic level using a multimodal approach is crucial to improving device performance because QDs are nanostructures with highly correlated structural parameters. In this study, scanning transmission electron microscopy, geometric phase analysis, and atom probe tomography were employed to characterize structural parameters such as the shape, strain, and composition of self-assembled InAs-QDs with InGaAlAs spacer layers. The measurements revealed characteristic AlAs-rich regions above the QDs and InAs-rich regions surrounding the QD columns, which can be explained by the relationship between the effect of strain and surface curvature around the QD. The methodology described in this study accelerates the development of future QD devices because its multiple perspectives reveal phenomena such as atomic-scale segregations and allow for more detailed discussions of the mechanisms of these phenomena.