Photo-elastic modulation Fourier transform spectrum (PEM-FTS) has the characteristics of fast modulation speed and large amount of information. However, because of the sampling position error and other reasons, there exists phase difference in the output interference data, which affects the accuracy of the reconstructed spectrum. Therefore, a phase correction scheme with high computing speed must be adopted. The 300K infrared blackbody was used as the radiant source in the experiment, and interference data were generated by the photo-elastic modulation interferometer. Mertz method is used to correct the phase of photo-elastic modulation interference data on the TMS320C6713 DSP (digital signal processor) chip. First a complete double interference data is extracted befroe the apodization processing to calculate the phase error of small double interference data, which takes the zero optical path as the center. Then a whole interference figure error phase is acquired with interpolating zero and the spectrum of the complete interference data and correcting phase are obtained at last . With two-norm to define the accuracy of corrected spectrum ,and using the method of calculating timer period register to count code running time, and observing program and data memory space in the file of command. The correction results of Mertz method and modulus square method were analysed comparatively. Experimental results show that Mertz method has advantages of fast speed, occupying less storage space and less correction error when implement phase correction on the DSP. And the operation time of Mertz phase correction method is 20 times faster than that of modulus square method.Consequently, it is suitable for high speed and accurate phase correction of PEM-FTS interference data.