A fingerprint analysis method was developed for the quality control of Citrus aurantium by high performance liquid chromatography(HPLC).The separation was carried out on a Waters Tnature-ACCHROM C18(4.6 mm×250 mm,5 μm) column,using acetonitrile-05% formic acid water as mobile phase by gradient elution,and the common peaks in the fingerprint of Citrus aurantium were identified by high performance liquid chromatography-quadrupole time of flight-mass spectrometry(HPLC-QTOF-MS).Similaritity evaluation,cluster analysis(CA) ,principal component analysis(PCA) and orthogonal partial least square discriminant analysis(OPLS-DA) were used for the data analysis and quality evaluation on 22 batches of Citrus aurantium.Results showed that 12 common peaks were defined by the fingerprint,and 11 components were identified by HPLC-QTOF-MS.The similarities for 22 batches of Citrus aurantium samples were more than 0.9.The results obtained from CA,PCA and OPLS-DA were consistent,among which,the samples from Jiangxi Province were clustered into one group,while the samples from Hunan Province and Fujian Province were clustered into another group,and three quality differential markers were screened out as hesperidin,neohesperidin and naringin by OPLS-DA.The HPLC fingerprint for Citrus aurantium is stable and reliable,and could be used to provide a reference for its quality control.