Abstract: This paper got the absorption spectrums of L-glutamic acid samples and arginine samples by THz time domain spectroscopy.At the same time,it got THz absorption spectrums of L-glutamic acid and arginine molecules by the quantum chemical calculation analysis software Gaussian09 and DFT theory calculation.Then,this paper compared the absorption spectrums of simulation and experiment and observed the position and number of absorption peak.THz time-domain spectroscopy is a new coherent detection technology because it has high noise ratio in the range of 3THz and no damage to the biological activity of molecular structure.The result of simulation agreed well with experiment,but the result of simulation as high frequency offset frequency.