On-orbit spectral calibration of hyperspectral imaging data is a key step for quantitatively analyzing them. Like the atmospheric correction, accurate spectral calibration is very necessary for improved studies of land or ocean surface properties. Based on the previous literatures, a new method which coupled an optimization algorithm was developed to simultaneously retrieve the central wavelength and the full width at half maximum (FWHM) of the hyperspectral sensor without needing the in situ reflectance spectra. Firstly, the Hyperion data set simulated using MODTRAN4 with the Hyperion spectral specification was used to test the new method, and the results indicated that the maximum error was less than 0.1 and 0.7 nm for central wavelength and FWHM respectively when the spectral shift is 5 nm. Then the algorithm was applied to the Hyperion data acquired on May 20, 2008 over Heihe River Basin and it was iteratively performed for each detector of the two spectrometers of Hyperion. The results showed that the VNIR of Hyperion had a pronounced smile effect, and the shift in on-orbit calibration with respect to the laboratory was from -2 to +2 nm, while the SWIR has essentially no smile effect, the wavelength correction was relatively flat over all sample with an approximately constant value of 3 nm. The FWHM in VNIR could range from -0.2 to 0.5 nm as a function of sample number of the spectrometer, and in SWIR it ranged from -2 to -3 nm. So for both the VNIR and SWIR, the original spectral calibration should be updated. These results showed good agreement with previous research findings, and which also proved the feasibility of the new method. Finally, with the updated spectral calibration characteristics, the sample reflectances of desert and vegetation target in our study site were reconstructed by applying a further atmospheric correction, and as expected, the strong spikes around the typical atmospheric absorption were almost disappeared.