Chromatographic analysis of flavonoids in ethyl acetate fractions of the stamen, gynoecium, and petal of Magnolia grandiflora L. by HPLC-PDA-MS/MS-ESI in the negative ionization mode was performed in this study. The results revealed the presence of eight flavonoids: apigenin 8-C-glucoside, luteolin 8-C-glucoside, quercetin 3-O-rutinoside, quercetin 3-O-galactoside, quercetin, 3-O-glucoside, kaempferol 3-O-rutinoside, isorhamnetin 3-O-glucoside, and isorhamnetin. Their quantification revealed that luteolin 8-C-glucoside is the major flavonoid and that the total phenolic content is concentrated primarily in the stamen. The antioxidant and hepatoprotective effects of ethanolic extract of the flower organs were evaluated against hepatotoxicity induced by CCl4, compared with the effects of silymarin.