To establish a new method to analyze IR fingerprint， which is in line with the characteristic of traditional Chinese medicine, two indexes， common peak ratio and variant peak ratio， were applied and their values were calculated by means of sequential analysis， in which each Cacumen platycladi sample’s IR fingerprint spectra were set up and the common peak ratio sequences were arranged in the order of size in comparison with other samples. The analytical results showed that samples G1 and G8 from the same region, and G4, G2 and G6 from the closer regions were the most similar samples with higher common peak ratio (≥90.0%) and lower variant peak ratio (≤11.1%). However， the samples G10, G3, G4 and G5 from the closer regions collected in different years， and G2 and G7 from the farther regions，were of significant disparity with common peak ratio less than 50% and variant peak ratio larger than 50%. As a result， the method could be used to distinguish Cacumen platycladi of different areas and batches. The dual index sequential analysis enables us to distinguish two or more herb’s IR fingerprints, is a new method to analyze IR fingerprint spectra， and can be used in line with the characteristics of traditional Chinese medicine.