Introduction: The correlation between the quality and geographical origin of herbal medicine was traced back to Tang Dynasty in China, more than 1200 years, and the effects of ecological environments on the secondary metabolites such as flavonoids have been confirmed. However, little is known about how the adversity impacts on the quality. Reactive oxygen species (ROS) may be medium between the ecological environment and the secondary metabolism. Materials and Methods: The fresh roots of Scutellaria baicalensis Georgi were treated with 0.002 μmol/L, 0.2 μmol/L, and 20 μmol/L H 2 O 2, respectively. A stress model was established to elucidate the change of secondary metabolism, anti-oxidant enzyme system, and enzymes relating to flavonoids. Results: The activities of superoxide dismutase, catalase and peroxidase decreased. Too much H 2 O 2, firstly, boosted transformation of flavonoids glycoside into aglucon with the most remarkable activities through UDP-glucuronate baicalein 7-O-glucuronosyltransferase (UBGAT), and β-glucuronidase (GUS), then regulated the gene expression of phenylalanine ammonialyase, GUS, and UBGAT, and increased the contents of flavones, motivated the flavonoid glycoside converting into aglucon. With this action, the flavones displaced the anti-oxidant enzymes. The higher the dosage, the more baicalein and wogonin increased, the later they took action. Conclusion: The plant secondary metabolites to keep ROS constant are identical to the effective materials in clinic. They are closely linked. H 2 O 2 can improve flavones, especially the aglucon, and further increased the quality of herbal medicine, which possesses very important value in medical practice.