Aiming at the characteristics of novel spatial heterodyne spectroscopy (SHS), the phase error mechanism is studied, and the actual phase of each wavelength is calculated using tunable lasers and the theoretical phase is acquired by frequency calibration, and the phase error is eliminated according to convolution in the frequency domain. Using measured interferogram of continuous light source by spectrometer and atmospheric absorption of CO2 interferogram, a phase error correction experiment is carried out. The experiment, correcting the phase error of continuous light source and atmospheric absorption of CO2 interferogram measured by spatial heterodyne spectrometer, shows that the phase error correction algorithm can achieve perfect result for spatial heterodyne spectrometer.