Gouqi, a commonly used traditional Chinese medicine, was studied by Fourier transform infrared (FTIR) spectroscopy in this paper. The combination of FTIR with mathematic method was used for the first time to classify the Gouqi from different cultural areas. It can be seen that the Gouqi samples from Ningxia Yuxi, Ningxia Zhongning and Neimenggu Tuoketuoqi could be successfully classified by soft independent modeling of class analogy (SIMCA). As having the fast and accurate characters, FTIR provides a new way to evaluate the origin of the Chinese medicines impersonally based on the traditional methods.