High‐altitude environments expose plants to increased levels of UV‐B radiation, necessitating the evolution of protective mechanisms to mitigate stress. Buckwheat is a flavonoid‐rich pseudocereal naturally adapted to high‐altitude environments with elevated UV‐B exposure. Although flavonoid biosynthesis is thought to contribute to this adaptation, the molecular and metabolic basis underlying flavonoid‐mediated UV‐B tolerance remains largely uncharacterized. In this study, we comprehensively assessed the relationship between flavonoid content and UV‐B resistance across several cultivated and wild buckwheat species, including Fagopyrum esculentum , F. tataricum , F. cymosum , F. gracilipes and F. urophyllum . Our findings demonstrate that the synthesis of rutin strongly correlates with enhanced UV‐B tolerance in buckwheat species, and the synthesis of rutin, along with isoquercitrin, positively influences the growth of diverse crops under UV‐B stress. Functional validation of key enzymes revealed that the G125D variation in FtFLS4 and variations within the PGSG‐box of FtRT1 significantly impact rutin‐related metabolite synthesis in buckwheat. Notably, the Tartary buckwheat genes FtFLS4 , FtUF3GT1 and FtRT1 exhibited both catalytic activity and UV‐B inducible promoter responses, collectively underpinning F. tataricum 's superior UV‐B tolerance. Furthermore, we characterised the distinct UV‐B response characteristics of FgFLS4 and FgFLS7 in the tetraploid wild buckwheat F. gracilipes , suggesting diversified adaptive strategies. Our findings provide novel insights into the functional basis of UV‐B adaptation in Tartary buckwheat and offer potential targets for breeding or engineering UV‐B‐resilient crops.