Hepatitis B Virus (HBV) infection is a global public health challenge that seriously endangers human health. Soft coral, as a major source of terpenoids, contains many structurally novel and highly bioactive compounds. In previous studies, it has been demonstrated that cembranoid-type diterpenoids showed significant anti-inflammatory and anti-colorectal cancer activities. In this study, cembranoids isolated from Sinularia pedunculata was found with anti-HBV activity for the first time. Among them, compound 6 showed significant anti-HBV activity with an IC50 value of 5.57 µM without cytotoxicity. We analysed the preliminary structure-activity relationship (SAR). Furthermore, it is demonstrated that compound 6 can accelerate the formation of capsid, inhibit HBeAg, HBV core particle DNA, HBV total RNA and pregenomic RNA in a dose dependent manner. We also confirmed the anti-HBV activity in HepG2-NTCP infection system. Finally, we find the anti-HBV mechanism of these compounds by inhibiting the ENI/Xp enhancer/promoter.