OBJECTIVE To establish the HPLC fingerprint of Mongolian medicine Sanzisan ，and to evaluate its internal quality by chemical pattern recognition technique comprehensively. METHODS HPLC method was used. Using geniposide as reference，HPLC fingerprints of 15 batches of Sanzisan were drawn with Similarity Evaluation System of TCM Chromatogram Fingerprint（2012 edition）. Similarity evaluation and common peaks identification were conducted. Combined with cluster analysis （CA），principal component analysis （PCA），and orthogonal partial least squares-discriminant analysis （OPLS-DA），the quality of 15 batches of Sanzisan was evaluated ，and the differential markers that affected its quality were screened. RESULTS There were 29 common peaks in 15 batches of Sanzisan ，and the similarity was no less than 0.952，indicating that the chemical composition of the 15 batches of Sanzisan had good consistency. A total of 13 common peaks were identified ，which were chebulic acid ，gallic acid，punicalin，punicalagin A ，punicalagin B ，jasminoside B ，caffeic acid ，corilagin，geniposide，chebulagic acid ，1，2，3，4，6- O-galloylglucose，chebulinic acid ，ellagic acid. Both CA and PCA could divide 15 batches of Sanzisan into four categories ，and the classification results were consistent ，indicating that the quality of 15 batches of Sanzisan had certain differences. Fourteen differential markers （chebulic acid ，gallic acid ，ellagic acid ，etc）that lead to the quality difference between batches were screened out by OPLS-DA. CONCLUSIONS Established HPLC fingerprint analysis method is simple and stable. Combined with chemical pattern recognition analysis ，it can be used for the quality control of Sanzisan.