In an apparatus and a method of measuring a thickness of a multilayer on a substrate, a spectrum of reflected light reflected from the substrate is measured. A plurality of recipe data, each corresponding to one of a plurality of hypothetical multilayers, is stored. One of the plurality of hypothetical multilayers is initially assumed to be the multilayer actually formed on the substrate. A plurality of theoretical spectra is calculated using one of the plurality of recipe data in accordance with various theoretical thicknesses of one of the plurality of hypothetical multilayers. The measured spectrum is compared with the plurality of theoretical spectra to determine a temporary thickness of the multilayer. A reliability of the temporary thickness of the multilayer is estimated. The temporary thickness is output as a thickness of the multilayer on the substrate when the reliability of the temporary thickness is within an allowable range.