Wavelength-tuning phase-shifting interferometry has advantages over conventional hardware phase-shifting for the simultaneous detection of all surfaces of the transparent parallel flats. The Fourier transform and its derivative methods can be used to characterize the signal based on the optical path difference and the phase-shifting value of the corresponding interferometric harmonic signals on each measured surface and to solve for the phase accordingly. Therefore, considering the influence of the sampling length and the choice of the window function in the Fourier transform on the measurement results, based on the established multi-surface interference model, an adequate simulation analysis is carried out, and the corresponding explanations and discussions are given subsequently. In practical measurements, the appropriate window function and sampling length should be selected according to the corresponding measurement conditions, so that reliable measurements can be guaranteed.