The entire phenolic profiles and antioxidant activities of different organs of the edible tree peony flowers (Fengdan Bai (FDB)) were analyzed. HPLC-quadrupole time-of-flight mass spectrometer (Q-TOF-MS/MS) analyses of individual phenolic compounds revealed that the petal and stamen contained higher levels of flavonoid glycosides than other organs (p < 0.05). Kaempferol-3,7-di-O-glucoside was the dominant flavonoid in these two organs, however, the calyx and ovary contained higher contents of gallic acid derivatives than other organs (p < 0.05). Hexa-O-galloyl-glucose was the dominant species in the calyx and ovary. At the same concentration of total phenolic extract (TPE), the stamen had the highest protection effect on Caco-2 cell oxidative damage induced by H₂O₂. The antioxidant effect was attributed to potent antioxidant capability; restored redox state due to the increased expression of glutathione peroxidase (GSH-Px) and superoxide dismutase (SOD); and improved barrier function of Caco-2 cell owing to increased zonula occludens-1 (ZO-1), CLDN3 (Claudin 3), and occludin mRNA expression. As a new resource food, the edible tree peony flower is a potential functional food material and natural antioxidants resource.