For the investigation of the interface stability of SrTiO3/Sr/Si(100) system during high temperature annealing process, we have grown 1—2 atom layer SrTiO3 ultra-thin film on Sr/Si(100)-2×1 substrate using pulsed laser deposition technique. After annealing, we found that nano-scale islands appear in the surface. These nano-islands show metallic property by scanning tunneling microscopy, and the STM image shows bias voltage dependence of these nano-islands. Oxygen in the oxide reacts with silicon and forms volatile silicon monoxide during vacuum annealing, while Ti atoms in the oxide react with silicon, forming C-54 TiSi2 islands.