The proliferation of ultraviolet (UV) light especially in the Tibetan Plateau, have a significant impact on agricultural ecosystems. Plants have inherent tolerance or capacity for acclimation and resistance to stressful environmental conditions, including those associated with climate change. Researching the mechanism of wheat response to UV radiation contributes to provide prospective proposals to cope with the UV radiation that crops are anticipated to be exposed to, especially in high-altitude localities. ZN168, a purple waxy and high yield common wheat line , pyramided the waxy loci selected by MAS was used for analysis. In the current study, the changes in wheat coleoptile photomorphogenic were observed under simulated high-level UV radiation in plant chambers. High-throughput sequencing on wheat coleoptile revealed that UV responses based on TaUVR8-mediated UV-absorbing metabolites (primary flavonoids and anthocyanins) biosynthesis and gene expression associated with photosynthesis and phenols metabolism, and these responses can trigger acclimatory processes to avoid further UV damage. Besides, metabolomics analysis on grains harvested in Chengdu and Lhasa (~30% higher UV radiation than ChengDu, and more than ten times anthocyanins content of seeds than Chengdu) revealed that UV radiation had a marked effect on anthocyanins accumulation. Furthermore, to gain insights into the regulatory networks related to flavonoids biosynthesis and identify key regulatory genes, an integrated analysis of the dynamic transcriptome and metabolome in developmental wheat grains were performed. Correlation tests of metabolites contents and transcriptional changes showed strong correlations between flavonoids compounds and transcripts categorized into flavonoid metabolism, hormones, transcriptional regulation, and signaling. The connection network of flavonoids and genes showed a regulatory system involved in the pigmentation of developmental wheat grains, suggesting that this systemic approach is powerful for investigations into novel genes that are potential targets for the breeding of new anthocyanin-enriched wheat cultivars. This study will enable us to exploit genes pinpointed as the targets of genetic engineering, thereby improving the UV tolerance of wheat. Furthermore, due to its UV-adaptive potential and nutrition, the anthocyanin-enriched wheat can be excellent resources to cope with the proliferating-level of UV radiation and act as functional food.