Bletilla striata (B. striata), a renowned traditional Chinese medicinal herb, has been widely utilized in the treatment of various diseases. Various secondary metabolites are the major bioactive ingredients in B. striata tubers, and their biosynthesis and accumulation are influenced by ultraviolet radiation. However, the mechanisms underlying UV-C radiation effects remain largely unclear. In the present research, we used a combined analysis of metabolome and transcriptome to investigate the physiological and bioactive component accumulation of B. striata under the UV-C treatment. The tubers average fresh weight decreased to d36 after being treated with UV-C irradiations. As measured by malondialdehyde (MDA) content, showed a significant increase in MDA content compared to control plants throughout the experiment (from d12 to d36). The activity of antioxidant enzyme superoxide dismutase (SOD) was up-regulated to varying degrees during radiation. However, catalase (CAT) and peroxidase (POD) showed a peak trend. The content of metabolites (chrysin, daidzein, calycosin, apigenin, sakuranetin, and desmthylxanthohumol) for flavonoid biosynthesis and phenylpropanoids biosynthesis significantly increased under the UV treatments. Concurrently, UV-C stress triggers 5476 DEGs; key defense genes show > 5-fold upregulation. Several important genes involved in flavonoid biosynthesis and phenylpropanoids biosynthesis, including phenylalanine ammonia-lyase (PAL), 4-coumarate: CoA ligase (4CL), cinnamic acid 4-hydroxylase (C4H), chalcone isomerase (CHI), and chalcone synthase (CHS), showed increased expression in EG. Our study provides the molecular biosynthesis underlying the effects of UV treatment on the biosynthesis of flavonoids and phenylpropanoids metabolites in B. striata and offers a theoretical basis for the artificial cultivation and industrial production of bioactive ingredients.