The formation process of silicon-nanocrystals (Si-NCs) in the amorphous silicon/silicon dioxide (a-Si/SiO2) multilayer structure during thermal annealing is theoretically studied with a modified model based on the Gibbs free energy variation. In this model, the concept of average effective interfacial free energy variation is introduced and the whole formation process consisting of nucleation and subsequent growth is considered. The calculating results indicate that there is a lower limit of the silicon layer thickness for forming Si-NCs in a-Si/SiO2 multilayer, and the oxide interfaces cannot constrain their lateral growth. Furthermore, by comparing the results for a-Si/SiO2 and a-Si/SiNx multilayers, it is found that the constraint on the crystal growth from the dielectric interfaces depends on the difference between interfacial free energies.