A white light spectral interferometry based on a Linnik type system was established to accurately measure the thin film thickness through transparent medium. In practical work, the equivalent thickness of a beam splitter and the mismatch of the objective lens introduce nonlinear phase errors. Adding a transparent medium also increases the equivalent thickness. The simulation results showthat the equivalent thickness has a significant effect on thin film thickness measurements. Therefore, it is necessary to perform wavelength correction to provide a constant equivalent thickness for beamsplitters. In the experiments, some pieces of cover glasses as the transparent medium were added to the measured beam and then a standard thin film thickness of 1052.2±0.9 nm was tested through the transparent medium. The results demonstrate that our system has a nanometer-level accuracy for thin film thickness measurement through transparent medium with optical path compensation.