HPLC fingerprint of Lycium chinense and the cluster analysis was used to evaluate Lycium chinense from different areas. The chromatographic fingerprints of Lycium chinense from 8 different origins were established by HPLC. “Similarity Evaluation System for Chromatographic Fingerprint of TCM” and SPSS 19.0 was applied to analyzing Lycium chinense samples from different regions. Results showed that fingerprints of flavonoids in Lycium chinense from different areas were specific, and the high similarities of the samples from Zhongning, Qinghai and Xinjiang were 1, 0.963 and 0.956, respectively, and they also got together in cluster analysis. Lycium chinense produced in Qinghai and Xinjiang were so similar to that in Zhongning, which could be the new source for medicine use. The method of HPLC fingerprint bonded with cluster analysis was able to provide a reference for the discrimination and quality evaluation of Lycium chinense.