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The imaging Fourier transform spectrometer (IFTS) carried on HJ-1A is the first spaceborne hyperspectral earth observation sensor in China Shifts in the spectral channel center wavelengths of IFTS may occur after launch due to vibrations, and to changes in instrument temperature and pressure. In this paper, we described an improved on-orbit spectral calibration method, which is based on spectrum angle matching between the spectrometer-measured radiance spectrum and the modeled radiance spectrum at atmospheric absorption bands Compared with the laboratory calibration result of IFTS, spectral shifts ranged from -3.18 to -3.4 nm were derived depending on cross-track spectral position at 760-nm oxygen bands, and from -3.53 to-3.79 nm at 820-nm water vapor bands With the updated spectral calibration coefficient, the reflectance of vegetation and desert in our study site were reconstructed by applying a further atmospheric correction, and the strong spikes around the atmospheric absorption bands were almost obviously suppressed.