With the common and variation peak ratio dual index sequence analysis method, using mean value, smoothness and derivative processing methods to calibrate and exclude interference, in order to increase resolution of spectrum, and then inspected the RSD of stability and repeatability of three different polarity solvent extracts of Gentiana rigescens, calculated the common and variation peak ratio in the UV fingerprint spectral, to evaluate the quality of G. rigescens from different areas. The results showed that, at 40 min, the extract ratio was the best in chloroform, absolute ethyl alcohol or water, and in 30h the RSD of stability respectively were between 0.078-0.455, 0.158-0.462, 0.052-0.682; the RSD of repeatability respectively were between 0.044-0.753, 0.156-0.288, 0.191-2.413. The fingerprint spectral implicated that the largest common peak ratio was 67.6%, while the least was 45.2%, and the largest variation peak ratio was 78.9%, the least was 21.7% among different areas of G. rigescens. The method could be used exactly in qualitative evaluation of two more herb samples, and clarified the similarity level among different areas, also applied the basement for authenticity identification and quality evaluation of herbs.