A method for estimating spatial carrier frequencies in the interferogram analysis using Fourier transform was presented. By multiplying the original interferogram with a 2D window function and calculating the centroid coordinates of the sidelobe of the apodized interferogram,the spatial carrier frequencies was estimated with high accuracy. Based on the Fourier shift theorem,the carrier removal was realized with the estimated spatial carrier frequencies. The simulation and experiment results show that the method can suppress the carrier removal error as well as the spectrum leakage error effectively.