Corydalis Rhizoma was taken as an example for demonstration research based on the concept of quality markers (Q-markers), confirmed standards and research modes were proposed by the author. The chemical constituents of Corydalis Rhizoma were identified using high performance liquid chromatography/electrospray ionization quadruple time-of-flight mass spectrometry (HPLC/ESI-Q-TOF MS). The source and specificity of chemical constituents were confirmed by analyzing biosynthetic pathway and component specificity. The major effective components were clarified through efficacy, drug property, pharmacokinetic studies, and correlation analysis of chemical constituents. The Q-markers were determined by integrating all the results of the studies. At last, seven alkaloidal compounds including tetrahydropalmatine, corydaline, coptisine, palmatine, dehydrocorydaline, tetrahydrojatrorrhizine, and protopine have been selected as Q-markers and quality control methods of multi-component assaying and fingerprint have been established.