Cortex Moutan (Paeonia suffruticosa Andr.) is a common traditional Chinese medicine and has been widely used in clinic for 2000 years in China. As sources for this crude drug are always mixed with other species, many cultivars on herbal market may lead to quality instability. Multi-component quantitative analysis is an efficient method to reflect chemical profiles of herb medicine and is always taken as the main method for quality evaluation. So, the aim of this work is to develop analytical method to quantify paeonol, paeoniflorin, gallic acid, oxypaeoniflorin, benzoylpaeoniflorin and paeonolide in Cortex Moutan (CM) to evaluate the chemical qualities of CM from different species or cultivars. Besides, we also study the intestinal absorption characteristics of paeonol and paeoniflorin for further pharmacological evaluation. In the present study, all of the standard markers were performed on an Ecosil C 18 (250 mm × 4.6 mm, 5 μM, Lubex Co., Guangzhou, China) with linear gradient elution of 0.2% formic acid water and acetonitrile. The proposed method was applied to analyze 50 batches of samples with acceptable linearity (R 2 , 0.9995-0.9999), precisions (RSD, 0.47%-2.08%), repeatability (RSD, 039%-2.63%), stability (RSD, 0.52%-2.45%), and recovery (RSD, 0.72%-3.03%) of the six compounds. Furthermore, the Hierarchical Cluster Analysis was applied to classify the 50 samples based on contents of the six compound markers. The results obtained from multi-component quantification of CM clearly indicated that CM originated from P. suffruticosa and P. ostii presented different chemical properties, and that samples from the two materials could be gathered into one branch, respectively, while CM sourced from cultivars of P. suffruticosa showed great variety on chemical quality. The results from Hierarchical Cluster Analysis implied that the established method could be used as a powerful tool for the quality evaluation of CM.