Attenuated total reflectance Fourier transform infrared spectrograph (ATR-FTIR) has become a common way to analyze and represent dyes as it can be used to acquire the far infrared spectra of powder samples (only less dosage) conveniently, easily, and sensitively apart from being able to identify the unknown samples in terms of their finger-print features. Five dyes, including ciba blue 2B, deoxyshikonin, indigo, 1H-Indole-2, 3-dione, and thioindigo, were measured by ATR-FTIR with the condition of vacuum. We acquired the absorption spectra within the region of 50~610 cm-1. The experimental results showed that there were obvious characteristic peaks in these five dyes and the corresponding peak positons were identified. And then Gaussian 09 software was used for simulating the vibrational assignments of thioindigo molecule and identifying the fingerprint spectra. It can be seen from the visualization results that the absorption peaks of thioindigo from 50~610 cm-1 were mainly caused by the collective vibration and the vibration modes ranged from low frequency to high frequency. Although the simulation results corresponded well with the experimental results, there were some differences between experimental and simulated results. For example, the values between experimental and simulated results were dissimilar; the positions of absorption peaks in the experiment shifted; the new peak positions were acquired in simulation. The main reason was that the temperature of simulation went far from that of experiment; the intermolecular activity was not considered in the theory calculation; the weak effect of contacting between the ATR crystal and powder; and the resolution of the instrument was not high enough.