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Flavonoids are the main components of Meconopsis integrifolia (Maxim.) Franch, which is a traditional Tibetan medicine. However, traditional chromatography separation requires a large quantity of raw M. integrifolia and is very time consuming. Herein, we applied high-speed counter-current chromatography in the separation and purification of flavonoids from the ethanol extracts of M. integrifolia flower. Ethyl acetate/n-butanol/water (2:3:5, v/v/v) was selected as the optimum solvent system to purify the four components, namely quercetin-3-O-β-d-glucopyrannosy-(1→6)-β-d-glucopyranoside (compound 1, 60 mg), quercetin 3-O-[2'''-O-acetyl-β-d-glucopyranosyl-(1→6)-β-d-glucopyranoside (compound 2, 40 mg), quercetin 3-O-[3'''-O-acetyl-β-d-glucopyranosyl-(1→6)-β-d-glucopyranoside (compound 3, 11 mg), and quercetin 3-O-[6'''-O-acetyl-β-d-glucopyranosyl-(1→6)-β-d-glucopyranoside (compound 4, 16 mg). Among the four compounds, 3 and 4 were new acetylated flavonol diglucosides. After the high-speed counter-current chromatography separation, the purities of the four flavonol diglucosides were 98, 95, 90, and 92%, respectively. The structures of these compounds were identified by mass spectrometry and NMR spectroscopy.