Similarity analysis of FTIR of Lapis Micae Aureum was carried out to find out the relationship between similarity of infrared spectra and the quality of medicine samples, and try to provide a new method for its quality assessment. FTIR was used to analyze Lapis Micae Aureum samples. Then 6 samples with good quality were picked up to establish a reference infrared spectra by their infrared spectra. Correlation coefficient method and the included angle cosine method were used to calculate the similarity between sample’s infrared spectra and the reference infrared spectra. For all those 19 samples with characters in accordance with Ch.P, the similarity is above 0.94, and for the others the similarity is less than 0.94. Although some samples’ source meets the requirement of Ch.P, but with poor quality by traditional experience, the similarity is lower than those of good quality. It was concluded that the similarity of infrared spectra of Lapis Micae Aureum is closely related to the quality of medicines. As a result, similarity analysis of FTIR of Lapis Micae Aureum is reliable, and can be used for its quality assessment.