Under the room temperature (293K) and nitrogen environment, the refractive index and absorption coefficient of the organophosphorus pesticide phosmet and hexachlorobenzene were measured by using the technology of terahertz time-domain spectroscopy within 0.3–2.3 THz. At the same time, density functional theory (DFT) was applied to calculate vibrational frequencies of the phosmet molecule and the hexachlorobenzene molecule in the terahertz region with Gaussian software. And then the experimental results and the theoretical results were compared, the result showed that phosmet and hexachlorobenzene had some characteristic absorption peaks, and among which, the absorption peaks in both theory and experiment are caused by intramolecular vibrations, while other absorption peaks in the experiment may be caused by weak intermolecular interactions, lattice vibrations and mixed vibrations. In addition, based on the results of theoretical calculation, the vibration models of phosmet and hexachlorobenzene in the THz band were identified by the visual software GaussView 5.0.8. At last, the research shows that THz-TDS technology is feasible for pesticide detection, and which lays the foundation for the application of THz-TDS system in pesticide identification and residue quantitative detection.