Alteration information extraction is one of the most important aspects of hypersepctral remote sensing application, and alteration mineral identification based on special absorption peaks is an important means of alteration information extraction. Due to the absorption and scattering of the atmosphere, atmospheric correction must be performed in order to obtain a more realistic reflection spectrum of the ground object. At present, comparison researches on atmospheric correction mainly focus on the improvement of image quality before and after atmospheric correction, the improvement of the classification effect of different features, and the correlation between the corrected image pixel spectrum and the actual spectrum. In contrast, the correspondence between absorption peaks of pixel spectrum obtained using different atmospheric correction and actual spectrum is rarely discussed, which is extremely unfavorable for geological application of hyperspectral remote sensing that is based on identification of mineral absorption peaks. In this study, the CASI-SASI aeronautical hyperspectral imaging system was used to collect the airborne hyperspectral data of the Longshoushan area of Gansu Province. Additionally, spectra of terrain objects were obtained using ground based ASD spectrometer. Based on these datasets, a geological application oriented comparison research on FLAASH, QUAC, and EMPL atmospheric correction methods was conducted. The results suggest that FLAASH, QUAC, and EMPL can eliminate the effects of the atmosphere and improve the image quality of aerial hyperspectral remote sensing, and EMPL shows the best effect. Besides, the absorption peaks of terrain objects’ reflection spectra and corresponded pixel reflection spectra obtained with different atmospheric correction were compared using visual interpretation. It is found that the absorption peaks of pixel spectra have different degrees of differences from those of the real terrain object spectra. Although EMPL has the best retention, some absorption peaks are still error corresponded, suggesting that multiple atmospheric correction methods should be used and a comprehensive research should be carried to improve the alteration extraction accuracy.