There is provided a method of measuring a physical thickness of each of layers of a multilayer film, based on an optical thickness thereof. The method includes: (a) setting refractive indexes of the layers; (b) calculating a coefficient matrix using the refractive indexes; (c) providing light to the multilayer film so as to measure the optical thickness based on the light reflected by the multilayer film; and (d) calculating the physical thickness, based on the optical thickness and the coefficient matrix.