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Abstract Background Methicillin-resistant Staphylococcus aureus (MRSA) causes serious infections in hospitals. Penthorum chinense Pursh (PCP), employed by the Miao ethnic minority in China, presents antibacterial activities. In this study, the anti-Staphylococcus aureus activities in the pinocembrin-7-O residue-rich fraction from PCP (PGF) were evaluated and characterized. Methods The PGF was prepared with 70% ethanol reflux extraction followed by fractional extraction and column chromatography. Pinocembrin-7-O residue components were identified with electrospray ionization mass spectrometry (ESI-MS). Anti-S. aureus activities of the fraction and the main components were evaluated in vitro with serially diluted microbroth assays. Cytotoxicity was evaluated with 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) chromogenic assays using the NCTC 1469 cell line. Results This study indicated that the PGF and three components (S1, S2, and S3) presented anti-S. aureus activities, including against clinically isolated MRSA strains. The molecular masses of S1, S2, and S3 were identical to those of pinocembrin-7-O-[4″,6″-hexahydroxydiphenoyl (HHDP)]-β-D-glucose, pinocembrin-7-O-[3″-O-galloyl-4″,6″-(s)-HHDP]-β-D-glucose, and Thonningianin A, respectively. The PGF, S1, S2, and S3 all presented an identical minimum inhibitory concentration (MIC) against S. aureus ATCC 25923 and ATCC 43300, which was 62.5 μg/mL. The minimum bactericidal concentrations (MBCs) of the PGF and S3 against ATCC 25923 were 125 and 250 μg/mL, and the MBCs of the PGF, S2, and S3 against ATCC 43300 were 250, 500, and 250 μg/mL, respectively. A time-kill assay consistently indicated that none of the bacterial clones of ATCC 25923 and ATCC 43300 could survive under 2× and 4× MIC PGF treatment for 24 h, respectively. In contrast, 104 CFU (colony-forming units) of ATCC 25923 and ATCC 43300 were killed by 8× and 4× MIC S3 within 24 h, respectively. Additionally, 1×, 2×, and 4× MIC the PGF presented similar postantibiotic effects (PAEs) on the strain ATCC 25923. However, the PAE of the PGF on the strain ATCC 43300 was concentration dependent (1×