Natural stilbenes have unique physiological effects, such as anti-senile dementia, anti-cancer, anti-bacterial, lowering blood lipid, and other important biological functions, which have attracted great attention from scholars in recent years. In this study, two stilbene compounds, resveratrol (RES) and polydatin (PD), were isolated from Mulberry (Morus alba L.), and their antioxidant activity and mechanism were investigated. The results showed that the contents of RES and PD in mulberry roots were 32.45 and 3.15 μg/g, respectively, significantly higher than those in mulberry fruits (0.48 and 0.0020 μg/g) and mulberry branches (5.70 and 0.33 μg/g). Both RES and PD showed high antioxidant potential by DPPH, ABTS free-scavenging methods, and ORAC assay, and provided protection against oxidative damage in HepG2 cells by increased catalase (CAT) activity, superoxide dismutase (SOD) activity, and Glutathione (GSH) content, and decreasing generation of reactive oxygen species (ROS), lactate dehydrogenase (LDH) level, and malondialdehyde (MDA) content. Therefore, RES and PD treatment could be effective for attenuating AAPH-induced oxidative stress in HepG2 cells. This study will promote the development and application of stilbene compounds. Furthermore, the RES and PD could be used as antioxidant supplements in functional foods, cosmetics, or pharmaceuticals, contributing to health improvement.