An SiO2/Si substrate has been widely used to support two-dimensional (2d) flakes grown by chemical vapor deposition or prepared by micromechanical cleavage. The Raman intensity of the vibration modes of 2d flakes is used to identify the layer number of 2d flakes on the SiO2/Si substrate, however, such an intensity is usually dependent on the flake quality, crystal orientation and laser polarization. Here, we used graphene flakes, a prototype system, to demonstrate how to use the intensity ratio between the Si peak from SiO2/Si substrates underneath graphene flakes and that from bare SiO2/Si substrates for the layer-number identification of graphene flakes up to 100 layers. This technique is robust, fast and nondestructive against sample orientation, laser excitation and the presence of defects in the graphene layers. The effect of relevant experimental parameters on the layer-number identification was discussed in detail, such as the thickness of the SiO2 layer, laser excitation wavelength and numerical aperture of the used objective. This paves the way to use Raman signals from dielectric substrates for layer-number identification of ultrathin flakes of various 2d materials.