Multilayered SiOx/SiO2 and SiOxNy/SiO2 thin films were fabricated using different techniques and subsequently annealed at high temperatures (≥1100 °C) in order to form Si nanocrystals by means of the well-known superlattice approach. The thickness of the SiOx and SiOxNy layers was varied from 1.5 to 5 nm, while for the SiO2 layers it was fixed at 4 nm. Using transmission electron microscopy, we showed that the multilayered structure generally sustains the high temperature annealing for both types of films. However, for samples with ultrathin SiOx or SiOxNy layers a breakdown of the superlattice structure and a complete intermixing of layers were observed at high temperatures. On the contrary, annealing at lower temperature (900 °C) preserves the multilayered structure even of such samples. Theoretical calculations showed that the intermixing of SiOx/SiO2 and SiOxNy/SiO2 superlattices in the ultrathin layers thickness limit may be explained thermodynamically by the gain in the Gibbs free energy, which depends in turn on the annealing temperature.