Introduction: The transformation of wild herbal medicine into cultivation results in decreased quality, becoming an issue of concern in China, even has a word, “traditional Chinese medical science would be destroyed by herbal medicine.” Now, there is no way to acquire superior herb medicine. Reactive oxygen species (ROS) are generated under stress and represent key plant products that induce secondary metabolism. ROS may be important intermediates that link environmental stress to secondary metabolism. Sodium hydrosulfite (Na2S2O4) is just one compound that produces O2•-. Materials and Methods: The fresh roots of Scutellaria baicalensis were treated with 0.0004, 0.04, and 4 mmol/L Na2S2O4, respectively. A stress model was established to elucidate the change of secondary metabolism, antioxidant enzyme system, and enzymes relating to flavonoids. Results: Na2S2O4regulated the activities of β-glucuronidase (GUS) and UDP-glucuronate baicalein 7-O-glucuronosyltransferase (UBGAT) and promoted the transformation of flavonoid glycosides into aglycones with greater antioxidant capacities. In fresh S. baicalensis roots, Na2S2O4decreased the activities of superoxide dismutase, catalase, and peroxidase (POD), which led to a substantial accumulation of hydrogen peroxide (H2O2). H2O2increased the expression of phenylalanine ammonia lyase, GUS, and UBGAT genes and promoted the synthesis and transformation of flavonoids. Moreover, polyphenol oxidase regulated the flavonoid content to maintain the oxidation balance. Although the content of flavonoid glycosides was slightly reduced, the total flavonoid content remained high. Notably, the content of baicalein, an antioxidant compound, increased from 0.28% to 1.96%. Conclusions: ROS facilitated the dominant role of secondary metabolites and enhanced the quality of Radix Scutellariae.