Thickness measurement of the thin films is crucial for chip manufacturing and integrated circuits. Ellipsometry has the advantage of high measurement precision. The ellipsometry parameters of the full spectrum can be obtained by utilizing the broad spectrum measurement method to realize the thickness measurement of the nano-scale films. In order to solve the problem of film thickness measurement on the transparent silicon substrate which is often seen in the semiconductor field and eliminate the superimposed signal of the silicon layer, this paper proposed a polarization separation spectral interference ellipsometry system. A Mach-Zehnder interferometer was built to achieve the thickness measurement of the film on the silicon substrate in the near-infrared band. Taking the silica film with a thickness of 100 nm as the specimen, the measurement precision of nanometer scale was achieved. The method proposed in this paper is applicable to the thickness measurement of the thin films on transparent or opaque substrates, which avoids the correction steps in the detection process or the change of the incident wavelength. It can be used in the high-precision detection of the finished products of film preparation processes and technologies such as chemical vapor deposition and molecular beam epitaxy.