Nyingchi City is located in the southeast of Qinghai-Tibet Plateau, which belongs to the mountain valley landform in the warm and semi-humid climate of the plateau, with a large vertical elevation drop and rich and unique wild buckwheat resources. A series of changes in temperature, humidity, air pressure, and ultraviolet intensity brought about by altitude changes can cause changes in plant morphology and metabolite content. In order to explore the relationship between functional traits of wild buckwheat and altitude, the wild buckwheat germplasm collected by the wild buckwheat expedition team of the Chinese Academy of Agricultural Sciences in Nyingchi City in October 2023 were investigated and collected, and five altitude gradients of 3,100m, 3,300m, 3,500m, 3,700m, and 3,900m were selected. To compare and analyze the morphological differences and flavonoid metabolite contents of wild Tartary buckwheat. The results showed that 1000-grain weight, grain length, grain width, grain diameter, grain perimeter, and grain area of wild Tartary buckwheat increased first and then decreased with the increase of altitude, reaching the maximum at 3700m altitude and significantly higher than other altitude gradients. There were also significant differences in the content of flavonoid metabolites in wild Tartary buckwheat at different elevation gradients: The contents of rutin and quercetin in wild Tartary buckwheat at 3900m altitude were significantly higher than those at other altitudes (p < 0.05). The contents of quercetin 7-O-glucoside, proanthocyanidins B1 and proanthocyanidins C1 in wild Tartary buckwheat at 3700m altitude were the highest, and the contents of proanthocyanidins in wild Tartary buckwheat at 3500m altitude were the highest. The highest content of kaempferol, cyanidin, afodaside, and pyroside was found in wild Tartary buckwheat at 3300m. The results analyzed the differences in the distribution and abundance, seed traits and flavonoid content of wild buckwheat under different altitude gradients, revealed the physiological mechanism of wild buckwheat in adapting to the ecological environment, laid a foundation for exploring the adaptive evolution of wild buckwheat, and also provided ideas for breeding buckwheat to resist adversity.