Density functional theory was used to optimize the geometry structure of two isomers of ginsenoside, Re, 20-(R)-R and 20-(S)-Re. The ginsenoside Re is an active constituent in ginseng. The calculated results show that there is an obvious difference in space structure between 20-(R)-R and 20-(S)-Re. The main reason for that can be the difference in the space orientation of the four constituents in the 20th carbon (chiral), which leads to the different stacking mode and causes the difference in vibrational spectra in the two isomers. The experimental IR and Raman spectra were assigned according to the calculated frequency, theoretical IR intensity and Raman active. The calculated vibrational peaks at 1 541, 1 456 and 1 424 cm^-1 can be used to distinguish the two isomers. The result shows a good agreement between the calculated and the experimental Raman spectra. The vibrational spectra can be used to identify the active constituent in ginseng.