Corydalis Rhizoma is the dried tuber of Corydalis yanhusuo W.T. Wang which is used in traditional Chinese medicine for pain relief and blood activation. Before being used in the clinics, C. yanhusuo is traditionally processed through dry-frying or frying with vinegar, wine or salt. In this study, eleven alkaloids from Corydalis Rhizoma, namely protopine (1), α-allocryptopine (2), tetrahydrocolumbamine (3), coptisine (4), palmatine (5), berberine (6), dehydrocorydaline (7), d,l-tetrahydropalmatine (8), tetrahydroberberine (9), corydaline (10) and tetrahydrocoptisine (11) were simultaneously quantified using a newly developed high performance liquid chromatography-diode array detector (HPLC-DAD) method. The influence of vinegar and wine processing on the content of the main alkaloids of Corydalis Rhizoma was investigated. For this purpose, two common formulations with clinical application, namely the water decoction of Corydalis Rhizoma and its formula Jin Ling Zi San (combination of Corydalis Rhizoma and Toosendan Fructus) were studied. In the two water decoctions, wine and vinegar processing increased the amount of tertiary alkaloids. The differences were more pronounced for Jin Ling Zi San, in which case the content of all tertiary alkaloids (compounds 1, 2, 3, 8, 9, 10, 11) was increased by wine processing.