To use molecular docking and dynamic simulation to investigate the inhibitory action of chlorogenic acid (CHA) and its analogues against sortase A of Staphylococcus aureus. Five novel, natural inhibitors with different activities were discovered for sortase A (SrtA). The inhibition mechanism of the novel inhibitors was consistent with the mechanism of CHA, which was reported previously by Wang et al. (Front Microbiol 6:1031, 2015). Based on structure-activity relationship analysis, the hydroxyl moiety (C1) of the inhibitors is critical in the catalytic region of SrtA, which could be confirmed by the calculation of the binding free energy between SrtA and the inhibitors. The mechanism obtained by molecular dynamics simulation is thus useful for the development of novel, selective SrtA inhibitors.