A dual-index sequential analysis method for analyzing the common and variant peak ratios of bulbus lilii in infrared fingerprint is established. The common and variant peak ratios of ten kinds of samples from different regions are measured and analyzed. The result shows that some bulbus lilii samples from several neighbouring regions all have higher common peak ratios and lower variant peak ratios in their infrared fingerprint. Some samples from several other neighbouring regions have the common peak ratios higher than 80.0% and variant peak ratios lower than 25.0%. Some samples from several regions which are far away from each other have the common peak ratios lower than 60.0% and variant peak ratios lower than 15.8%. This analysis method is simpler and more effective than the chromatographic analysis method. It can discriminate the bulbus lilii from different regions accurately and will become a new method for evaluating the quality of traditional Chinese medicine.