The effects of enhanced ultraviolet-B(UV-B) radiation on chemical compositions of radix, stem and leaf of Scutellaria baicalensis Georgi were studied via FTIR. Results showed that alcohols and phenolic substances in the radix and leaf of S. baicalensis Georgi were increased by UV-B radiation as well as the content of flavonoids and flavonoids glycosides. The terpenoids content in radix and protein content in leaf were increased by supplementary UV-B radiation. Contrary to the circumstance in radix and leaf, contents of alcohols and phenolic, flavonoids, unsaturated fat and lactone in stem were decreased by UV-B radiation. These results indicated that there is a trade-off in distribution of the metabolites in radix, stem and leaf of different parts. More information could be revealed for the result of FTIR spectral analysis via FTIR second derivative spectrum, especially the information of the combination between flavonoids and glycosides. The effects of UV-B radiation on chemical composition in radix, stem and leaf of S. baicalensis Georgi could be examined simply and rapidly via the method of FTIR. Thus, it can be used as a prior method before the further analysis of chemical composition.