Abstract: Abstract: Terahertz radiation is the electromagnetic wave, which occupies a large portion between the infrared and microwave bands. Most biological macromolecules have fingerprint characteristics in this band. Firstly, the device for experiment i.e. the terahertz time-domain spectroscopy system (THz-TDS) was introduced. Then, in order to seek the terahertz spectrum characteristics of transgenic mechanism and the trait expression, 3 kinds of transgenic cotton seeds (Zhongmian No.838, Lumianyan No.28, and Guoshen No.7886) and a non-transgenic cotton seed (Xinluzao No.51) were studied in identifying experiments by terahertz time-domain spectroscopy. Because of the grease-like substance in the cotton seed, tablet mold was occlusive when compressing cotton seed. It made the tablet shaping difficult and the surface of the tablets rough and resulted in unperfect data. To solve the problem, when compressing tablet, a small amount of polyethylene powder was taken to spread in the bottom of the compression mould, then samples powder was spread on polyethylene powder, and then on the surface of samples powder a small amount of the powdered polyethylene was put again, and at last the tablet was compressed. During the experiment, the samples were placed in the THz-TDS to scan and reduce the accidental error. Each tablet was scanned in triplicate for different parts and the obtained spectral information is averaged. To avoid the interference such as the strong absorption of the water vapor and other polar molecules in the air, terahertz wave generation and detection device were sealed and filled with dry nitrogen. And the relative humidity of testing environment was less than 4%. The experimental temperature was kept at 298 K. By using terahertz time-domain spectroscopy equipment, we collected the terahertz spectral information of 4 species of cotton seeds in the effective time-domain range. After processed with the fast Fourier transform algorithm, THz spectroscopy time-domain information was transformed into the frequency-domain spectral information. Then a series of transformations were used to get their refractive index and absorption spectra. Qualitative analysis of the terahertz spectrum feature information was made. Terahertz absorption characteristics of 4 kinds of samples especially in 0.9-1.5 THz band and the reasons for this result were discussed in detail. The results showed that 4 kinds of cotton seeds presented different spectral response characteristics in 0.9-1.5 THz band. The 3 transgenic cotton varieties showed obvious absorption at 1.21, 1.23 and 1.41 THz, while non-transgenic cotton variety showed weak absorption or no absorption.