The effect of annealing time on the InSb nanocrystal formation in a silicon-on-insulator structure, containing, near the Si/SiO2 interface, Si and SiO2 regions implanted with Sb+ and In+ ions, respectively, was studied. The annealing temperature was 1100 °C. A change in the nanocrystal growth direction was obtained as the annealing time increased from 1 to 90 min. After the 1 min annealing, the InSb nanocrystals grew within the Si matrix and were faceted. As the annealing time increased to 90 min, the nanocrystals grew from the Si/SiO2 interface into the SiO2 matrix; they had a half-spherical shape. A respective change in the phonon mode was observed, too. The origin of the obtained effect is discussed.