Chemical investigation of the deep-sea-derived fungus Aspergillus versicolor SCSIO 41502 resulted in the isolation of three new anthraquinones, aspergilols G-I (1–3), one new diphenyl ether, 4-carbglyceryl-3,3′-dihydroxy-5,5′-dimethyldiphenyl ether (4), and one new benzaldehyde derivative, 2,4-dihydroxy-6-(4-methoxy-2-oxopentyl)-3-methylbenzaldehyde (5), along with 23 known phenolic compounds (6–28). The structures of new compounds were elucidated by extensive spectroscopic analysis. The absolute configuration of 3 was established by CD spectrum and the modified Mosher method. Compounds 2, 3 and 9 had evident antiviral activity towards HSV-1 with EC50 values of 4.68, 6.25, and 3.12μM, respectively. Compounds 15, 18, 20 and 22–24 showed more potent antioxidant activity than l-ascorbic acid with IC50 values of 18.92–52.27μM towards DPPH radicals. Comparison of the structures and antioxidant activities of 1–28 suggests that the number of phenolic hydroxyl group that can freely rotate can significantly affect the antioxidant activity of phenolic compounds. In addition, 4, 22–24 and 27 had significant antifouling activity against Bugula neritina larval settlement with EC50 values of 1.28, 2.61, 5.48, 1.59, and 3.40μg/ml, respectively.