As the basic building block for photonic device integration, silicon nanophotonic waveguide requires low-loss propagation for high-performance ultra-compact photonic device. We experimentally study SiO2 grown by two different methods (thermal oxidation and PECVD) as hard masks for Si nano-waveguides fabrication and study their effects on propagation loss. It was found that the denser and smoother quality of thermally grown SiO2 will increase the etch selectivity of Si and reduce the line-edge roughness transferred to the Si nanowaveguide sidewall, hence giving a lower loss compared to having PECVD SiO2 hard mask. With thermally grown SiO2 as hard mask, the Si nano-waveguides loss can have a loss reduction as high as 5.5 times for a 650 nm wide nanowaveguide. Using thermally grown SiO2 as hard mask will allow the Si nano-waveguide to have as low a propagation loss as direct resist mask and enable III-V semiconductor on silicon via bonding for multifunctional photonic system on chip.