Spatial heterodyne spectroscopy (SHS) is a new spectroscopic technique which can achieve high spectral resolution. The basic concepts of spatial heterodyne spectrometer are described. The two-dimensional (2D) interference fringe distortion is due to asymmetry of double optical path, which caused by the errors from optical systems of the interferometer. According to the characteristics of SHS interference fringe distortions, a SHS interferogram correction method based on frequency domain analysis is presented. The corrected coordinate of fast Fourier transform (FFT) frequency domain signal obtained from monochromatic source calibration. Then the calibration curve fitting from corrected coordinate can be used for correction of SHS interferogram. Spectral experiments are operated on the SHS instrument by monochromatic source and Gaussian continuous spectrum source. The experimental results show that the correction method can effectively remove interference of system asymmetry, correct 2D SHS interferogram and improve spectral inversion accuracy of spatial heterodyne spectrometer.