Corydalis Rhizoma is the tuber of Corydalis yanhusuo W. T. Wang, which has been long used in traditional Chinese medicine. Herein, the quality of C. yanhusuo samples collected from 23 regions of three provinces in China is evaluated through high-performance liquid chromatography fingerprinting coupled with similarity, hierarchical clustering, and principal component analyses. Sample similarities are evaluated according to the State Food and Drug Administration requirements by selection of 18 characteristic chromatographic fingerprint peaks and are found to vary between 0.455 and 0.999. Moreover, common patterns of a typical local variety of C. yanhusuo sourced in the Panan County are established. The obtained results show that the combination of quantitative analysis and chromatographic fingerprint analysis can be readily utilized for quality control purposes, offering a comprehensive strategy for quality evaluation of C. yanhusuo and related products.