The shape changes in GaAs nanocrystals deposited on Si substrate have been studied as a function of the coverage by transmission electron microscopic observations in order to see the growth mechanism from the viewpoint of the surface energy and the lattice strain energy between the nanocrystal and the substrate. When GaAs was deposited on the Si(100) surface, the shape of the GaAs nanocrystals changes from stepped mound, hut cluster to dome structure with increasing the coverage. The shape changes are responsible for decreasing the total free energy caused by the lattice strain energy with the substrate and surface energy depending on the crystal size.