In this study, we established a comprehensive high‐performance liquid chromatography coupled with diode array detection and high‐resolution mass spectrometry method to identify 10 and quantified eight constituents in Corydalis Decumbentis Rhizoma (“Xiatianwu” in Chinese) and Corydalis Rhizoma (“Yanhusuo” in Chinese). Chemometric methods were applied to distinguish the botanical origins of the Xiatianwu and Yanhusuo samples. Chromatographic separation was achieved using an Agilent Poroshell EC‐C18 column with mobile phases A (1000 ml of 0.2% acetic acid solution containing 2.8 ml of triethylamine) and B (acetonitrile) and stepwise gradient elution. The analytical method was fully validated in terms of linearity, sensitivity, intra‐ and interday precision and repeatability, the limit of detection, the limit of quantitation, and recovery. Twenty‐six Xiatianwu samples and 10 Yanhusuo samples were analyzed for quality evaluation. In addition, hierarchical clustering analysis and principal component analysis were used to discriminate among samples of different botanical origins. The results showed that the contents of eight alkaloids in Xiatianwu and Yanhusuo were significantly different. Moreover, it was found that chemometric methods could be applied to accurately distinguish these two often conflated Chinese medicinal materials. In conclusion, this study provides a relatively comprehensive method for botanical origin identification and Xiatianwu and Yanhusuo quality control.