Thermal agglomeration of an ultrathin Si layer in silicon-on-insulator structures with a thickness ranging from 1 to 15 nm has been studied by atomic force microscopy. We found that the size of Si islands formed by agglomeration depends on the initial thickness of the Si layer, i.e., the height and the lateral size of Si islands increase with increasing Si thickness. Because the critical temperature for the agglomeration, however, is lower for thinner Si, the thickness dependence of Si island features is accompanied by a temperature effect. A calculation model based on both strain energy and surface free energy qualitatively explains most of the observed agglomeration phenomena, i.e., island formation and ordering.