Terahertz time-domain spectroscopy system was used to measure the characteristic absorption spectra of 8 transgenic cotton seeds in the frequency range from 0.3 to 1.5THz. Comparing the similarities and differences of THz absorption spectrum of 8 kinds of transgenic cotton seeds, which based on spectral analysis, and used principal component analysis to perform qualitative analysis, the relevant data of spectral analysis was obtained. Three principal component factors were extracted in this paper, of which the cumulative percentage variance reached 71.537%. Therefore, different categories of transgenic cotton seeds were clearly distinguished according to principal component analysis score chart. The experimental results indicated that nondestructive testing of transgenic cotton seeds could be achieved by using Terahertz time-domain spectroscopy system technology, which could be widely applied in the fields of agricultural seed selection, agricultural security and so on.