To screen for high-activity tartary buckwheat raw materials, this study compared the bioactive component retention and physicochemical properties of tartary buckwheat flour from Gansu, Shanxi, Yunnan, and Sichuan provinces under different milling times. The cortex structure of Gansu tartary buckwheat was dense, with a degree of milling of <15% after 6 min (compared with >15% after 3 min for samples from other regions). Its retention of bioactive components was significantly superior to those of tartary buckwheat from other regions; after 6 min of milling, the rutin content decreased by only 8.66% (compared with 43.44% after 3 min in in Sichuan tartary buckwheat), and quercetin decreased by 35.2% (compared with 47.25% after 3 min in Shanxi tartary buckwheat ). The reduced starch content in samples from all four regions remained within the range of 25.00%~28.00%; however, the estimated glycemic index (eGI) increased significantly (P<0.05). The eGI of Gansu tartary buckwheat increased the slowest (by only 1.96% after 3 min of milling), while that of Shanxi tartary buckwheat increased the most rapidly under the same milling time (by 5.36%). In addition, Gansu tartary buckwheat exhibited a high swelling capacity. Therefore, tartary buckwheat flour from Gansu retains more nutritional bioactive components and demonstrates better edible quality. The flour obtained after 6 min of milling was the most suitable raw material for developing high-activity tartary buckwheat foods. This study provides a theoretical basis for the precision processing of high-activity tartary buckwheat products.