Abstract: This paper presents the investigation of the THz spectra of chlorophyll of masson pine leaf, chlorophyll a and b standard sample by using Fourier transform infrared spectroscopy(FTIR)and density functional theory(DFT), in order to study the vibration and rotation of chemical bonds in chlorophyll molecule at THz frequencies, which will be used to identify the components in mixing biological samples. The frequency shift characteristic of THz spectra of chlorophyll due to the change of molecular structure will efficiently detect the development of pine wilt disease. The THz spectra of the extracted chlorophyll of masson pine leaf display a strong absorption at 2.86 THz, and weak absorption at the same frequency occurs for chlorophyll a standard sample, and chlorophyll b standard sample, which originates from porphyrin ring and phytol in the chlorophyll structure. In the other frequencies, the absorptions were not distinct. Based on the absorption performance of chlorophyll, we can identify the mixing biological samples. We studied the theoretical mechanism of absorption frequencies for chlorophyll by terms of DFT. The calculated results indicate the vibration and rotation originated from intermolecular interactions have more important effect on the THz absorption spectra compared with intramolecular interactions.