The hepatitis B virus (HBV) is the major cause of liver disease, and it develops into cirrhosis, chronic hepatitis, and hepatocellular carcinoma. Medicinal plants are traditional medicine and are used to cure several diseases. In this study, antioxidant assay by DPPH, total phenolic and flavonoid contents of Syzygium aromaticum and Olea europaea extracts, and their anti-viral effect against HBV. The chemical profile of the most active extracts was analyzed by LC/MS/MS, investigating the anti-HBV activity of methanol extracts for reducing the relative HBV replication in infected HepG2 cells with archived serum samples compared with other tested extracts of the two plants. The results proved that S. aromaticum methanol extract has higher phenolic and flavonoid content (150.71±1.24 mgGAE/g extract, 310.61±0.67 mg Rutin/g extract, respectively) than O. europaea methanol extract (108.77±1.17 mg GAE/g extract, 93.14 ± 2.11 mg Rutin/g extract, respectively). S. aromaticum has higher antioxidant activity than O. europaea (16.85 ± 0.81 and 36.62 ±1.17µg/ml). Nevertheless, the most potent anti-HBV extract in both plants was methanol. Hence, LC/MS/MS Fingerprint exhibited the presence of six compounds in O. europaea methanol extract including oleuropein, oleuropein glucoside, Rutin,and p-Coumaric acid while, S. aromaticum methanol extract exhibited ten compounds include caffeic acid, ellagic acid, galloyl glucose, and isobiflorin. So, both plants demonstrated promising anti-HBV activity. These findings suggest that both S. aromaticum and O. europaea hold promise as sources of anti-HBV agents, deserving further exploration for developing novel therapeutics against HBV infection.