To obtain a high precision spectrum, the interferogram of space heterodyne spectrometer should be corrected. This study proposes a correction method based on the Fourier transform to address the nonuniform distortion of the interferogram caused by defects in a spatial heterodyne spectrometer. The target spectrum is discovered theoretically to be the convolution of the Fourier transform of the nonuniform distortion and the distortion spectrum. A verification experiment os performed by taking the continuous optical water vapor interferogram as an example. The results show that, among 2693 sets of experimental data, 2679 sets of data obtained an obvious correction effect. The standard deviation of 3 sets of randomly selected data after a correction increased by the order of magnitude, which verifies the effectiveness of the correction method.