The microstructure and strain characteristics of self-assembled InAs/GaAs quantum dots (QDs) were studied by using transmission electron microscopy. Compressive strain was induced to uncapped QDs from GaAs substrate and the misfit strain largely increased after the deposition of GaAs cap layer. Tensile strain outside QD was extended along the vertical growth direction; up to 15 nm above the wetting layer. Vertically nonaligned and aligned stacked QDs were grown by adjusting the thickness of GaAs spacer layers. The QDs with a lens-shaped morphology were formed in the early stage of growth, and their apex was flattened by the out-diffusion of In atoms upon GaAs capping. However, aligned QDs maintained their lens-shaped structure with round apex after capping. It is believed that their apex did not flatten because the chemical potential gradient of In was relatively low due to the adjacent InAs QD layers.