Based on the frequency domain white light microscopic interferometry, this paper provides a non-linear phase noise reduction method to effectively increase the accuracy in the measurement of the thin film thickness, with the Linnik type system structure. This paper firstly outlines the system structure and the basic principles for the measurement of the thin film thickness, and explains the major non-linear phases component in the interference spectrum signal and their sources in detail, including those from the thin film itself and the non-linear phase noise from the effective thickness of beam splitter prism and the mismatch between the two objectives for the system. To mitigate such effect of noise, this paper corrects the effect of the non-linear phase noise on the measurement resulting from effective thickness based on the wavelength correction theory, and proposes the method for extracting the non-linear phase noise from the mismatch between two objectives. Finally, the extraction of non-linear phase noise is conducted by the experiment based on the above method. And the standard thin film verification test for the thickness measurement demonstrates that both the wavelength correction theory and the extraction method of non-linear phase noise can effectively increase the accuracy of the measurement.