The structural diversity of natural products provides a major source for discovering antimicrobials with novel structures or mechanisms to overcome microbial resistance. Herein, we prepared a series of rutaecarpine-pyridinium quaternary ammonium conjugates by using rutaecarpine as the lead compound. Bioactivity evaluation demonstrated that 5dl exhibits outstanding antibacterial activity against S. aureus ATCC 29213 and clinical MRSA isolates, with MIC values ranging from 0.5 to 2 μ