SiO_2/Si substrate has been widely used to support two-dimensional (2-D) crystal flakes grown by chemical vapor deposition or prepared by micromechanical cleavage. The visibility of 2-D flakes is very sensitive to the thickness of the SiO_2 layer (hsiO_2), which can not be determined precisely after the deposit of 2-D flakes. Here, we demonstrated a simple, fast and nondestructive tech- nique to precisely determine hsiO_2 of SiO_2 films on Si substrate only by optical contrast measurement with a typical micro-Raman confocal system. Because of its small lateral resolution down to the micrometer scale, this tech- nique can be used to access hsiO_2 on SiO_2/Si substrate that has been partially covered by 2-D crystal flakes, and then further determine the layer number of the 2-D crystal flakes. This technique can be extended to other dielectric multilayer substrates and the layer-number determination of 2-D crystal flakes on those substrates.