In this study, we aim to investigate the secondary metabolites from the coral-derived fungus Scopulariopsis sp. SCSIO 41229, which were collected from the Beibu Gulf. The secondary metabolites were isolated by silica gel column chromatography, reverse phase silica gel column chromatography, thin layer chromatography (TLC) and high-performance liquid chromatography (HPLC). The chemical structures of these compounds were identified by nuclear magnetic resonance (NMR), mass spectrometry (MS) and literature analysis. Nine known compounds were isolated and elucidated as neocyclocitrinols A–D (1~4), penicillenol A2 (5), cyclo-(D-Phe-L-Ile) (6), cyclo-(L-tryptophyl-L-phenylalanyl) (7), 2-(hept-5-enyl)-3-methyl-4-oxo-6,7,8,8a-tetrahydro-4H-pyrrolo[2,1-b]-1,3-oxazine (8), (8E,10E)-7-oxo-8,10-heptadecadienoic acid (9). Bioassays indicated that compounds 2, 4 had weak antioxidant activity and compounds 1, 4, 8 showed weak inhibitory activity against acetylcholin esterase. Compounds 1~9 were obtained from the fungus Scopulariopsis sp. for the first time.