Abstract: The "unclear substances and mechanisms" underlying the efficacy of Chinese material medica is a bottleneck limiting its modernization and internationalization. As the fundamental attribute that reflects the efficacy of Chinese material medica, the concept of "Five flavors" serves as the theoretical basis guiding its clinical application. Chemical biology, utilizing target fishing technology and molecular interaction analysis, has become a comprehensive approach to elucidate the targets and underlying molecular mechanisms of Chinese material medica. This review focuses on studies of the effective substances found in bitter-propertied Chinese material medica as an example to explore chemical biology strategies based on the flavors of Chinese material medica, providing a research perspective for interpreting effective substances through the lenses of the "Five flavors" theory.