The geostationary interferometric infrared sounder (GIIRS) on-board FY-4A satellite is an infrared Fourier transform spectrometer. To improve the quantitative application level of observed data, it is necessary to conduct the on-orbit spectral calibration of the GIIRS accurately. Since the spectral positions are determined by the reference laser frequency and the number of the sampling points collected from interferograms for the Fourier transform spectrometer, the key of the spectral calibration is to ensure the stability of the reference laser frequency. In this study, a line-by-line radiative transfer model (LBLRTM) is used to calculate the reference atmospheric absorption spectra. The effective sampling frequency of the laser is determined empirically by comparing the root-mean-square error between the observed and the reference spectra of the detector, achieving the on-orbit high-precision spectral calibration of the detector. This method is used for the on-orbit spectral calibration of the GIIRS on-board FY-4A satellite, clearly demonstrating its application value.