Compared with the infrared analysis of amino acids, terahertz wave has lower electronic energy and can be used for nondestructive testing. The intramolecular atomic vibration, the intermolecular hydrogen bond and the low-frequency vibration of the crystal lattice of amino acids are all in terahertz band, which makes them have absorption peaks in terahertz band, and different amino acid molecules have different Terahertz Absorption peaks. Therefore, this fingerprint characteristic of amino acids in terahertz band can be used for qualitative analysis of amino acids. Quantum chemical analysis methods can apply the basic principles and methods of quantum mechanics to study the structure, properties and relationships of stable and unstable molecules. It can also study the interactions, collisions and reactions between molecules. The Terahertz Absorption Spectra of amino acids can be calculated by quantum chemical calculation method, which can match the molecular vibration mode of the terahertz absorption peaks of amino acids. It has certain reference and directivity for the qualitative analysis of amino acids, and provides theoretical support for the terahertz time domain spectra of samples obtained from experiments. Quantum chemical calculation is carried out on the basis of the terahertz absorption spectra obtained from experiments. It can also validate the experimental results. In this paper, Terahertz Absorption Spectra of glutamine, threonine and histidine were obtained by terahertz time-domain spectroscopy. The monomolecular configurations of these three amino acids in the form of amphoteric ions were constructed respectively. The Terahertz Absorption spectra were simulated by quantum chemical calculation method after the structural optimization was completed. The calculated results showed that the Terahertz Absorption Spectra of three amino acids are quite different from those obtained by experiments, but the peak positions at high frequencies are basically the same. GaussView was used to observe the vibration and rotation of the absorption peaks of the three amino acids at the corresponding frequencies in the terahertz band. It was found that the functional groups of the three amino acids only rotated without vibration in the high frequency band, and the rotation modes were basically the same. The Terahertz Absorption Spectra of amino acid functional groups were calculated quantum chemistry. The vibration and rotation patterns of functional groups at the corresponding frequencies of the absorption peaks in the high frequency band were compared with those of three amino acid molecules at the corresponding frequencies of the absorption peaks in the high frequency band. The results showed that in the terahertz absorption spectra calculated by quantum chemistry method under the single molecular configuration of amino acids, the simulated absorption peaks calculated in the high frequency band are basically consistent with the experimental Terahertz Absorption peaks. Vibration mode analysis showed that the vibrational modes of amino acid functional groups of glutamine, threonine and histidine were the same in the terahertz high frequency band. The absorption peaks of the three amino acid molecules in the high frequency band mainly came from amino acid functional groups. Therefore, the qualitative analysis of amino acids can be realized by combining quantum chemical calculation with Terahertz Absorption spectrum.