Marine fungi represent a huge untapped resource of natural products. The bio-activity of a new asperbutenolide A from marine fungus Aspergillus terreus was not well known. In the present study, the minimum inhibitory concentration (MIC) and RNA-Sequencing were used to analyze the bio-activity and sterilization mechanism of asperbutenolide A against clinical pathogenic microbes. The results showed that the MICs of asperbutenolide A against methicillin-resistant Staphylococcus aureus (MRSA) were 4.0-8.0 μg/mL. The asperbutenolide A present poor bio-activity against with candida. The sterilization mechanism of asperbutenolide A against MRSA showed that there were 1426 differentially-expressed genes (DEGs) between the groups of MRSA treated with asperbutenolide A and negative control. Gene Ontology (GO) classification analysis indicated that the DEGs were mainly involved in cellular process, metabolic process, cellular anatomical entity, binding, catalytic activity, etc. Kyoto Encyclopedia of Genes and Genomes (KEGG) classification analysis showed that these DEGs were mainly enriched in amino acid metabolism, carbohydrate metabolism, membrane transport, etc. Moreover, qRT-PCR showed similar trends in the expressions of argF, ureA, glmS and opuCA with the RNA-Sequencing. These results indicated that asperbutenolide A was with ideal bio-activity against with MRSA and could be as a new antibacterial agent.