Fourier transform infrared (FTIR) spectroscopy and second derivative IR spectroscopy were applied to analyze and evaluate different parts of Scorpio. The second derivative IR spectra show clear differences while the origin spectra are quite similar. It was found that proteins are the dominant components in each part and the tail has distinct proteins compared to the others; fats are mainly stored in the trunk; sulfates are ubiquitous in all parts. Interestingly, the back part of the trunk of degenerative Scorpio contains some purine. It was demonstrated that FTIR spectroscopy integrated with second derivative IR spectroscopy not only can offer a fast, comprehensive and objective methodology for analyzing and evaluating the micro-differences among the various parts of same medicinal materials, but also can provide a rational guidance for medicinal and pharmacological studies.