Four new ruthenium polypyridyl complexes with prenyl groups, [Ru(bpy)2(MHIP)](PF6)2 (Ru(II)‐1), [Ru(dtb)2(MHIP)](PF6)2 (Ru(II)‐2), [Ru(dmb)2(MHIP)](PF6)2 (Ru(II)‐3), and [Ru(dmob)2(MHIP)](PF6)2 (Ru(II)‐4) (bpy = 2,2′‐bipyridine, dtb = 4,4′‐di‐tert‐butyl‐2,2′‐bipyridine, dmb = 4,4′‐dimethyl‐2,2′‐bipyridine, dmob = 4,4′‐dimethoxy‐2,2′‐bipyridine, and MHIP = 2‐(2,6‐dimethylhepta‐1,5‐dien‐1‐yl)−1H‐imidazo[4,f][1,10]phenanthroline), were synthesized and characterized. Their antibacterial activities against Staphylococcus aureus were assessed, and the minimum inhibition concentration (MIC) value of Ru(II)‐2 against S. aureus was only 0.5 µg/mL, showing the best antibacterial activity among them. S. aureus could be quickly killed by Ru(II)‐2 in 30 min and Ru(II)‐2 displayed an obvious inhibitive effect on the formation of a biofilm, which was essential to avoid the development of drug‐resistance. Meanwhile, Ru(II)‐2 exhibited a stable MIC value against antibiotic‐resistant bacteria. The antibacterial mechanism of Ru(II)‐2 was probably related to depolarization of the cell membrane, and a change of permeability was associated with the formation of reactive oxygen species, leading to leakage of nucleic acid and bacterial death. Furthermore, Ru(II)‐2 hardly showed toxicity to mammalian cells and the Galleria mellonella worm. Finally, murine infection studies also illustrated that Ru(II)‐2 was highly effective against S. aureus in vivo.