Objective To assess the relative contributions of postharvest processing and geographical source to phytochemical variation of Corydalis Rhizoma, and rhizome of Corydalis yanhusuo, and to examine what phytochemical components are the most sensitive to the differences of each factor and how they change. Methods HPLC fingerprinting and LC-MS coupled with chemometric approaches were applied. Results The results of principal component analysis(PCA) and hierarchical cluster analysis(HCA) explicitly demonstrated the postharvest processing could produce a greater impact on the phytochemical profiles of Corydalis Rhizoma than geographical source. The contents of most compounds increased after water boiling while decreased after sulphur-fumigation.Protopine, coptisine, and palmatine were the most variable components in processing. Geographical sources also led to a remarkable phytochemical differentiation, in which the environmental variation of the three regions might play a role. Dehydrocorybulbine, coptisine, dehydrocorydaline, and protopine varied most among the three production regions and decreased sequentially in Zhejiang, Shaanxi, and Jiangsu provinces, China. Conclusion Both postharvest processing and geographical source should be enhanced with the priority for the former in the quality control of Corydalis Rhizoma. The application of boiling is supported but the consistency should be improved in practice. Sulphur-fumigation is strongly suggested to be abandoned. Objective To assess the relative contributions of postharvest processing and geographical source to phytochemical variation of Corydalis Rhizoma, and rhizome of Corydalis yanhusuo, and to how to phytochemical components are the most sensitive to the differences of each factor and how they change. Methods HPLC fingerprinting and LC-MS coupled with chemometric approaches were applied. Results The results of principal component analysis(PCA) and hierarchical cluster analysis(HCA) substantially demonstrated the postharvest processing could produce a greater impact on the phytochemical profiles of Corydalis Rhizoma than geographical source. Of most compounds increased after water boiling while decreased after sulphur-fumigation.Protopine, coptisine, and palmatine were the most variable components in processing. Geographical sources also led to a distinguished phytochemical differentiation, in which the environmental variation of the three regions might Role. Dehydrocoryb Ulbine, coptisine, dehydrocorydaline, and protopine varied most among the three production regions and decreased steps in Zhejiang, Shaanxi, and Jiangsu provinces, China. Conclusion Both postharvest processing and geographical source should be enhanced with the priority for the former in the quality control of Sulphur-fumigation is strongly suggested to be abandoned. Corydalis Rhizoma. The application of boiling is supported but the consistency should be improved in practice. Sulphur-fumigation is strongly suggested to be abandoned.