Flavonoids from plants are particularly important in our diet. Buckwheat is a special crop that is rich in flavonoids. In this study, four important buckwheat varieties, including one tartary buckwheat and three common buckwheat varieties, were selected as experimental materials. The total flavonoid content of leaves from red-flowered common buckwheat was the highest, followed by tartary buckwheat leaves. A total of 182 flavonoid metabolites (including 53 flavone, 37 flavonol, 32 flavone C-glycosides, 24 flavanone, 18 anthocyanins, 7 isoflavone, 6 flavonolignan, and 5 proanthocyanidins) were identified based on Ultra Performance Liquid Chromatography-Electrospray Ionization-Tandem Mass Spectrometry (UPLC-ESI-MS/MS) system. Through clustering analysis, principal component analysis (PCA), and orthogonal signal correction and partial least squares-discriminant analysis (OPLS-DA), different samples were clearly separated. Considerable differences were observed in the flavonoid metabolites between tartary buckwheat leaves and common buckwheat leaves, and both displayed unique metabolites with important biological functions. This study provides new insights into the differences of flavonoid metabolites between tartary buckwheat and common buckwheat leaves and provides theoretical basis for the sufficient utilization of buckwheat.