Objective To study the secondary metabolites and their antibacterial activities from a marine-derived fungus Aspergillus sp. SWMU-WZ04-3. Methods The secondary metabolites from the fermented extracts of the fungus Aspergillus sp. SWMU-WZ04-3 were separated and purified by silica gel， gel column chromatography， semi-preparative high performance liquid chromatography and other modern chromatographic analysis methods. The structures of the compounds were identified by Nuclear Magnetic Resonance （NMR） analyses and Mass Spectrometry （MS） spectroscopic data， and by comparing with the data in previous literatures. Their antibacterial bioactivities were tested by disk diffusion method. Results Nine compounds were isolated from the fermentation broth of Aspergillus sp. SWMU-WZ04-3 and identified as 3，4-dimethoxyacetophenone （compound 1）， ethyl （2E）-3-（4-hydroxy-3-methoxyphenyl） prop-2-enoate （compound 2）， 4‐methyl‐5，6‐dihydropyren‐2‐one （compound 3）， 3，15-dihydroxyl-（22E，24R）-ergosta-5，8（14）， 22-trien-7-one （compound 4）， 9，12-octadecadienoic acid （Z， Z）-2，3-dihydroxypropyl ester （compound 5）， 1'-Hexadecanoic acid-2'，3'-dihydroxy-propylester （compound 6）， 2-（4-Hydroxyphenyl）ethyl 2，2-dimethylpropanoate （compound 7）， （22E， 24R）-stigmasta-5， 7， 22-trien-3-β-ol （compound 8）， β-sitosterol （compound 9）， respectively. In vitro biological activity results showed that compound 4 exhibited inhibitory effect against Escherichia coli at a concentration of 1 mg/mL， while other compounds had no obvious antibacterial activity. Conclusion Compounds 2， 5， 6 were isolated from Aspergillus sp. species for the first time， compound 4 has anti-Escherichia coli activity. The fungus Aspergillus sp. SWMU WZ04-3 has value in the further studys.