Red Toon is a popular vegetable of favorable health benefits over Asia and Russia regions. In this study, isolation and identification of chemical constituents were performed to assess the quality of this functional food cultivated in various origins or harvested in different months. As a result, eight flavonol glycosides including rutin (I), myricitrin (II), quercetin-3-O-β-d-galactoranoside (III), quercetin-3-O-β-d-glucopyranose (IV), quercetin-3-O-α-l-arabinopyranoside (V), astragalin (VI), quercetin-3-O-α-l-rhamopyranoside (VII), and kaempferol-3-O-α-l-rhamopyranoside (VIII) were obtained. Among these, compounds III and V were isolated from Toona genus for the first time. Importantly, a rapid and convenient ultra-performance liquid chromatography (UPLC) method was developed to quantify the flavonol glycosides in Red Toon and validated for linearity, precision, stability, repeatability, and accuracy successively. In addition, it was found that total flavonoid glycosides (about 2.6%) in the food were kept at a higher level from April to June than other months of the year. Furthermore, their content in the Red Toon collected from ten different origins was also determined and compared, and the results suggested that the total flavonoid glycosides from Shandong Yantai were the highest, followed by Shandong Ximou, supporting a well-recognized viewpoint that Red Toon cultivated in Shandong Province, China, is considered genuine due to the best health benefits and flavor.