One Polypyridyl Pd(Ⅱ) complex (Pd1) containing modified morpholine group was synthesized from 4’-［4-(4-morpholinobutyloxy) phenyl］-2,2’∶6’,2’-tripyridine and characterized by 1H NMR, element analysis and single crystal X-ray diffraction. The antibacterial activity of Pd1 was investigated against S. aureus with the MIC (minimum inhibition concentration) value of 62.48 μg/mL and the effect of Pd1 complex on S. aureus growth was investigated by growth curves. Bacteria resistance development assay indicate that the S. aureus cannot easily develop drug-resistance to Pd1. In addition, Pd1 complex can strengthen the susceptibility of S. aureus to clidamycin hydrochloride when it is combined with clidamycin hydrochloride. Meanwhile, Pd1 has a significant inhibitory effect on biofilms related to drug resistance, and show obviously inhibitory activity against the toxins from S. aureus.