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Four new lactones, including hypomonacid A (1) and hypomonone A–C (4–6), as well as nine known polyketide analogues (2–3 and 7–13) were obtained from endophytic fungus Hypomontagnella sp. TX-09 derived from Santalum album. Their planar structures were extensively established by analysing HRESIMS and NMR spectroscopic data. Stereochemistry of new compounds was determined by X-ray diffraction analysis and modified Mosher’s method in combination with quantum-chemical ECD calculation. In addition, compounds 1 and 2 showed anti-inflammatory activity by inhibition of lipopolysaccharide (LPS)-induced NO production in RAW264.7 cells at 50 μmol/L without cytotoxicity. Among them, compound 1 inhibited the production of LPS-stimulated inflammation in mouse macrophage RAW264.7 cells by suppressing the expression of iNOS, TNF-α, IL-1β, and IL-6.