With the rapid development of the transgenic biotechnology, more and more transgenic plants have been poured into the market, and scientists have paid much attention to transgenic plants' ecological safety. To analysize the content of organic matter and total nitrogen in rhizosphere of transgenic cottons and their parents, the dried soil were scanned by continuous wave of near infrared diffuse reflectance spectroscopy ranging from 12,000 to 4 000 cm(-1) with a resolution of 4 cm(-1) and scanning for 64 times. Bruker OPUS software was applied for quantification. This method was compared with the standard methods. The results showed that the precision of NIRS was very similar to the standard methods. On the other hand, the results also showed that the contents of organic matter and total nitrogen in rhizosphere soil of transgenic cottons were significantly higher than those of their parents, which could arise from the foreign toxin secretion of root.