Caulis spatholobi and caulis sargentodoxae are two different kinds of traditional Chinese medicine, which are similar to each other in appearance, but they are from differ sources with different functions.. This paper presents their spectrum using terahertz time-domain spectroscopy technology combines spectral matching algorithm to identify five different kinds of these samples. Due to the complex chemical composition of traditional Chinese medicine, different components of the characteristic absorption peak occurred easily mutually overlapping, therefore, it’s very difficult to find obvious characteristic absorption peak in terahertz range, caulis spatholobi and caulis like this. Every sample was measured 10 times in some position. These standard spectral data have been calculated in different frequency, data show good stability in range of 0.2~1.3 THz. The second order differential method is used to process the THz spectrum data from 0.2~1.3 THz. These tiny differences of absorption coefficient have been hemerged between caulis sargentodoxae and caulis spatholobi and compare with these data using the method of correlation coefficient block coding method, spectral angle method and information divergence method, respectively. The analysis results, the spectral angle method is the best algorithm, the discriminate accuracy of a total of 100 sets of data is 95%. It is a new way to distinguish difference of traditional Chinese medicine.