Abstract: The ten batches of Zhou's prescription extract that contains herbs that were collected from different cultivation areas and at different harvest times, and their HPLC fingerprint were established and simultaneously compared with standard reference.Zhou's prescription extract, which were obtained from Daodi cultivation areas, were selected as the standard chromatogram. The three chemometrics methods including hierarchical cluster analysis ( HCA) , principal component analysis ( PCA) and principal component-hierarchical cluster analysis ( PC-HCA) were used to compare difference of quality evaluation with similarity.Results showed that 32 peaks were selected as the common peaks in fingerprint, and common peak 5, 6, 9, 16, 17, 18, 20, 21, 24 and 27 was Catechin, Chlorogenic acid, Hydroxysafflor yellow A, Rutin, Hyperin, Luteolin-7-O-β-D-glucoside, Quercitrin, Apigenin-7-O-β-D-glucoside, Baicalin and Quercetin, respectively.It was difficult to reflect comprehensively the difference of Chinese herbal compound prescription by using the fingerprint similarity, and the above three chemometrics methods can evaluate objectively the quality of Chinese herbal compound prescription from various angles.