Investigation on Swertia mussotii resulted in four compounds by means of various chromatographic techniques (silica gel, Sephadex LH-20, RP-LC and Pre-HPLC). Their structures were determined as (S,2E,6E)-4,8-dihydroxy-2,6-dimethylocta-2,6-dienoic acid (1), (S,2E,6E)-8-(formyloxy)-4-hydroxy-2,6-dimethylocta-2,6-dienoic acid (2), swerimilegenins B and C (3 and 4) on the basis of extensive spectroscopic analyses including MS, IR, UV, 1D-and 2D-NMR. Among them, compounds 1 and 2 are two new linear monoterpenoids named as swerimusic acids C (1) and D (2), compounds 3 and 4 are two unusual known secoiridoid aglycones of C 9-skeleton obtained for the first time from this plant. Compounds 1~4 were evaluated for their anti-Hepatitis B Virus (HBV) activities on HepG2.2.15 cells line in vitro, but these compounds showed no anti-HBV activity at the maximal tesing concentration. Herin, we only report the isolation and structure elucidation of these compounds.