Flos Chrysanthemi Indici (FCI) is a Chinese herbal medicine used in China for over 2000 years. In this study, its ethanol extract (EFCL) was found to protect against hydroxyl radical (·−OH) induced oxidative damages to mesenchymal stem cells (MSCs) and DNA. To explore the mechanism, EFCL was further determined by chemical and antioxidant assays. Folin–Ciocalteu colorimetric assay suggested that content of total phenolics was 93.85 ± 3.56 mg catechin/g and HPLC analysis indicated a content of 10.05 ± 1.44 mg/g as chlorogenic acid in EFCI. Antioxidant assays revealed that EFCI could also scavenge ·−O2− radical (IC50 58.74 ± 1.30 μg/mL), DPPH·− radical (IC50 46.46 ± 1.35 μg/mL) and ABTS+·− radical (IC50 20.59 ± 0.52 μg/mL), bind Fe2+ (IC50 364.27 ± 19.57 μg/mL) and Cu2+ (IC50 734.77 ± 34.69 μg/mL), reduce Fe3+ (IC50 147.11 ± 11.09 μg/mL) and Cu2+ (IC50 35.69 ± 3.14 μg/mL). On the basis of mechanistic analysis, we concluded that FCI can effectively protect against hydroxyl-induced damages to DNA and MSCs, therefore FCI shows promise as a possible therapeutic reagent for many diseases. The effect may be mainly attributed to phenolics especially chlorogenic acid, which exerts the antioxidant action possibly through metal-chelating, and radical-scavenging which is via hydrogen atom transfer (HAT) and/or sequential electron proton transfer (SEPT) mechanisms.