We explored the mechanism of gene damaged by Auger electron using the Raman spectroscopy. The primers of the gene of alpha fetoprotein were labeled with radioactive iodine-125,and combined the gene of alpha fetoprotein. After the Auger electron emitted from iodine-125 radiated on gene two hours,the Raman spectroscopy was applied to investigate the influence of Auger electron to the biogenic conformation and functional groups in aqueous solution,with 514.5 nm excitation. The results show that the peak of the characteristic Raman spectra moves and the peak intensity changes with the Auger electron radiation from 2 hours to 24 hours. The change of Raman spectra indicates that the construction of the phosphodiester linkage harmed,the pyridine and purine bases in DNA emerged and damaged,the model of gene conformation changed from B form to C form spectrum. In conclusion,the Auger electron closely radiation may change the construction of backbone of DNA,destroy local pyridine and purine bases in DNA,and change the conformation of gene.