Fourier transform infrared spectrometer can be realized in high temperature flue gas multicomponent measurement at the same time,has wide application prospects in the field.And one of the important factors to determine the success of application,lies in the measuring system of infrared interference figure sampling phase error control.This paper discusses the main reasons of the appearance of phase error in the system,through the analysis of Helium-neon laser interference signal zero uniformity,illustrates the produce phase error is the main reason of the laser signal and reference signal phase difference.At the meantime,the quantitative analysis of the phase error influence on instrument signal to noise ratio(SNR),also the Mertz phase correction method for the instrument improves the thousands of times of the original signal to noise ratio.And the related experiment,the experimental results show that the system based on the interference figure sampling method satisfy the needs of high temperature flue gas measurements.