Magnolia (Magnoliaceae) is widely cultivated for its beauty; however, despite this, the components of the different flower colors in Magnolia have not been elucidated. In this study, the color parameters of 10 Magnolia petals with different colors were measured by the Royal Horticultural Society Color Chart (RHSCC) and a color reader CR-10. The composition and content of the flavonoids in the petals were analyzed by high-performance liquid chromatography coupled with diode array detection (HPLC-DAD) as well as HPLC with electrospray ionization and mass spectrometry (HPLC-ESI-MS2). All results showed that the 10 petals were divided into four color groups. Regarding the flavonoid composition, four types of anthocyanins, including Cyanidin-glucosyl-rhamnoside (Cy-GR), Cyanidin-glucosyl-rhamnosyl-glucoside (Cy-GRG), Peonidin-glucosyl-rhamnoside (Pn-GR), and Peonidin-glucosyl-rhamnosyl-glucoside (Pn-GRG), were identified, as well as 10 types of flavonols. The flavonols included isorhamnetin, quercetin, kaempferol, and their glycosides, which included rutinoside, rhamnose, and glucoside. Cyanidin and peonidin make Magnolia petals appear red-purple and purple, respectively, and the flavonols perform as evident auxiliary pigments, particularly quercetin. The Magnolia cultivar flower phenotypes sampled in this study differed by changes in their existing flavonoid content rather than by the appearance of new flavonoids. Consequently, this study provides a reference for further revealing the basis of Magnolia flower color and provides clues for color breeding.