Using the anti-hepatitis B virus (HBV)-producing cell line MS-G2 in vitro cultural system-guided screening was performed, and two new benzophenones, 2,6-dihydroxy-4-[(E)-5-hydroxy-3,7-dimethylocta-2,7-dienyloxy]benzophenone (1) and 2,6-dihydroxy-4-[(E)-7-hydroxy-3,7-dimethylocta-2-enyloxy]benzophenone (2), a new xanthone, hyperxanthone (3), a new bisanthraquinone glycoside, R-(-)-skyrin-6-O-beta-D-xylopyranoside (4), and 2-caffeoyloxy-3-hydroxy-3-(3,4-dihydroxyphenyl)propyl alcohol (5), and 16 known compounds were isolated from the anti-HBV active fraction of the whole herbs of Hypericum sampsonii. Their structures were elucidated using spectroscopic methods, mainly 2D NMR and MS spectrometry. Circular dichroism was used to determine the stereochemistry of bisanthraquinone glycosides.