Realgar is a mineral Chinese medicine, which has been used in China for thousands of years. A well-known truth is that the quality of traditional Chinese medicines is the basis for their efficacious and reliable roles for clinical use, which is principally determined by elements including the location of production and inner inorganic elements composition. However, there are few studies on the quality control of Realgar at present. Colon cancer, a severe malignant tumor, is known to have a poor prognosis due to a high rate of metastasis. So far, the effects of Realgar against colon cancer have not yet been clarified. An appropriate X-Ray Diffraction (XRD) method was used to systematically analyze the Realgar medicinal material samples. Fourier fingerprint combined with similarity evaluation, hierarchical cluster analysis, and principal component analysis was performed to assess and classify the samples on account of the XRD Fourier data. Cell viability, wound-healing, transwell migration, and matrigel invasion assays were performed. Western blotting was applied to determine the expression of the epithelial-mesenchymal transition (EMT) and MMPs relevant protein levels. Our explorations showed that the XRD Fourier fingerprints of Realgar medicinal material samples that had the same phase revealed 15 and 12 common peaks, respectively. The similarity evaluation of the established XRD Fourier fingerprint was greater than 0.900, which indicated that the XRD Fourier fingerprints of Realgar medicinal material were successfully established. Our study demonstrated that Realgar inhibited the proliferation, migration, and invasion of colon cancer cells. Realgar suppressed the EMT process and decreased MMP-9 and MMP-2 levels, which could be the reason for Realgar to inactivate colon cancer cell migration and invasion. Our findings could be applied in the quality control of Realgar and strongly demonstrate that Realgar could be a potential anti-tumor agent for colon cancer treatment.