Interferograms in the photo-elastic modulator Fourier transform spectrometers（PEM-FTS)has high modulation frequency, and its modulated optical path difference is continuous nonlinear. In order to improve the accuracy and stability of the rebuilt spectrums whose interferograms is sampled by the equal time intervals, it is necessary to study the technology of pretreatment and phase correction of photo-elastic modulated interferograms. In the paper, the characteristic that the amplitude of the zero optical path difference was maximum in a interferogram were used to derive these data of a interferogram. Simultaneously, the method which combined the improved Mertz method and the accelerated nonuniform fast Fourier transform algorithm (NUFFT) was put forward to resolve the asymmetric and to improve the velocity and precision of the rebuilt spectrum. In the experiment, the asymmetrical photo-elastic modulated interferograms of 300 K infared blackbody were generated by simulation, the data processing algorithm was applied to enhance the accuracy of the rebuild spectrum, and the atmosphere spectral curve was rebuilt and gas components were qualitative analyzed with the atmosphere window as the measured object.