Introduction: Chinese mineral medicine plays an important part in Traditional Chinese Medicine and has a long history, such as using Gypsum Fibrosum. Aim of our study is to establish a new Gypsum Fibrosum identification method and compare Gypsum Fibrosum and CaSO4 with the help of Fourier Transform Infrared spectroscopy (FTIR). Materials and methods: Determination and analysis of batches of Gypsum Fibrosum samples to establish the fingerprint by the OPUS acquisition system obtained from the German Bruker TENSOR 37 Fourier transform infrared spectroscopy, and then compare the Gypsum Fibrosum and CaSO4 by initial characteristic spectrogram, first derivative spectrum and second derivative spectrum. Results: The similarity of twenty-four samples were calculated by SPSS20, which showed that the correlation coefficient of twenty-four batches of samples was more than 0.980, except for No.16. There were distinctions of the wave number, peak position, spike and peak intensity between Gypsum Fibrosum and CaSO4 in the derivative spectroscopy. In view of the difference between Gypsum Fibrosum and CaSO4, a conclusion may be that there is a structural change. Discussion: Gypsum Fibrosum can be studied by FTIR and differences obtained between mineral medicine and the analytical reagent on the analysis of sulfate mineral. In addition, the result shows that it can provide a new, rapid and specific method for identification of Gypsum Fibrosum by FTIR.