In order to measure the infrared spectrum accurately, a high-precision Fourier Transform Infrared spectroscopy（FTIR）data processing system has been established. Some methods, such as apodization, phase correction, and wave number correction were researched. Compared with the two sides of window functions, Fourth-order Blackman window function was used for apodization of the interferogram, using convolution of unilateral interferometers for phase correction according to the characteristics of infrared interferometers phase error, further researched the number of wave energy calibration method of gravity wave number correction. Experimental results show that the spectra can be accurately measured by the Fourier transform infrared spectroscopy data processing system, and the accuracy of the wave number can increase 5 to 10 times under the condition of the wave number overlaps seriously, and the parameter would improve more than 103 times when the overlapping condition of the wave number is not serious. The Fourier transform infrared spectroscopy data processing system could meet the challenge of accurate measurement of the infrared spectrum.