Methicillin-resistant Staphylococcus aureus (MRSA) is a major causative agent for common infectious diseases in the world. With the emergence of antibiotic resistance in clinical therapy, there is an urgent need to develop novel antimicrobial drugs that will overcome these shortfalls. Secondary metabolites of endophytic fungi are important sources of antimicrobial drug mining as they serve as alternative synthetic antibiotics due to their safety and multi-target efficiency. Suberanilic acid, an amide alkaloid from the endophytic fungus Pestalotiopsis trachycarpicola DCL44, has been identified as an important antimicrobial agent, however, the antibiotic properties of suberanilic acid on multi-drug resistant bacterial such as MRSA has not been fully investigated. Therefore, to investigate the potential antimicrobial mechanism of suberanilic acid against MRSA, a quantitative proteomics approach using tandem mass tagging (TMT) was used. The results demonstrated that suberanilic acid had multiple targets of action against MRSA, which included affecting ribosome synthesis, inhibition of membrane translocation of nutrient uptake (ABC transporter system), and energy metabolism of carbohydrates, and amino acid metabolism dysregulation. In conclusion, this study demonstrates that suberanilic acid has the potential to be used as an antimicrobial agent for the control of MRSA infections and provides a reference for the development of antimicrobial agents of endophytic fungal origin.