A new fabrication technology for three-dimensionally buried silica on silicon optical waveguide based on deep etching and thermal oxidation is presented. Using this method, a silicon layer is left at the side of waveguide. The stress distribution and effective refractive index are calculated by using finite element method and finite different beam propagation method, respectively. The results indicate that the stress of silica on silicon optical waveguide fabricated by this method can be matched in parallel and vertical directions and stress birefringence can be effectively reduced due to the side-silicon layer.