In the retrieval of atmospheric trace-gas concentrations, it’s a widely used method to fit the calculated reference spectra to the measured spectra with least-squares methods. However, because of inaccuracies of the grating position, thermal changes in the spectrometer, and resolution differences between the two spectra, there is a spectral misalignment between the measured spectra and the reference spectra, that is the measured spectra may be shifted or stretched/squeezed. These misalignments will affect the accuracy of the retrieval. An algorithm for the shift-and-squeeze spectral correction in the process of the retrieval is introduced and the concentration error caused by spectral shift under different resolutions is calculated.