In this study, Panax notoginseng samples were extracted by chloroform, ethanol and water, or by those extracted solution with 5% vanillin sulfuric acid to establish two kinds of UV fingerprint of P. notoginseng which were compared by applying the common and variation peak ratio dual index sequence analysis method and SIMCA software qualitative analysis. The results indicated that the optimization extraction time of P. notoginseng samples was 20 min with chloroform, ethanol and water extraction, but the fingerprint differed significantly after add vanillin sulfuric acid. The common peak ratios of UV fingerprint of P. notoginseng were scattered. The minimum was 25%(Y5—Y8), while the maximum was 84.38%(Y11—Y13, Y20—Y21). The maximum variation peak ratio was 177.78%(Y8—Y5), meanwhile, the variation peak ratios of several samples were more than 100%. However, the common peak ratios of UV fingerprint of P. notoginseng with vanillin sulfuric acid were concentrated (distributed in the range of 50%～70%): the minimum was 42. 86%(Y1—Y19), whereas the maximum was 79.55% (Y22—Y23); the range of the variation peak ratios was also smaller with the ranges of 20%～50% in general. The result of the dual index sequence analysis was agreement with the fingerprint implied. The similarity of the UV fingerprint of the extracts of P. notoginseng after adding vanillin sulfuric acid was greater than before. Both the ages and origin was related with the difference of UV fingerprint. The similarity of the two samples with same age was more significant than those with different ages. The similarity and difference between samples was no correlation with the distance of geographic space, the near origin samples maybe have a significant similarity or difference. This method appears as good alternative for evaluate quality of the P. notoginseng and can distinguish at least two samples quantitatively, duo to it reaches the limitation of the multiple methods which only could be used to indistinctly distinguish herbs.