To address the emergency caused by multi-drug resistant Staphylococcus aureus, a series of novel capsaicin derivatives with nitrothiophene substituents have been designed and evaluated for the antibacterial activities against S. aureus Newman and multidrug-resistant strains (NRS-1, NRS-70, NRS-100, NRS-108, and NRS-271). The structure-activity relationship was further revealed. Compound 13c, 13f, and 13g were highly active against staphylococcal growth, with minimal inhibition concentration (MIC) values of 0.39-1.56 μg/mL. The oxadiazole-derived compound 21, a bioisostere of ester 13f, is the most potent candidate for anti-growth of five multidrug-resistant S. aureus strains with MICs of 0.20-0.78 μg/mL, which is more active compared with vancomycin in vitro. Notably, these anti-staphylococcal compounds are much less cytotoxic to the normal kidney epithelial cell line (HK293T).