A film thickness measuring system measures thicknesses of first films of respective first substrates by spectroscopy, captures first image data of surfaces of second substrates each having a second film to acquire first color information of the surfaces of the second substrates, and calculates a correlation between a thickness of the second film and color information of the surface of the second substrate by using the measured thickness of the first films and the first color information. When estimating a thickness of a third film of a third substrate, the film thickness measuring system acquire second color information of the surface of the third substrate by using captured image data of the third substrate, and estimates a thickness of the third film in the second region, by using the calculated correlation and the second color information.