Plant flavonoids have attracted increasing attention as new antimicrobial agents or adjuvants. In our previous work, it was confirmed that the cell membrane is the major site of plant flavonoids acting on the Gram-positive bacteria, which likely involves the inhibition of the respiratory chain. Inspired by the similar structural and antioxidant characters of plant flavonoids to hydro-menaquinone (MKH2), we deduced that the quinone pool is probably a key target of plant flavonoids inhibiting Gram-positive bacteria. To verify this, twelve plant flavonoids with six structural subtypes were preliminarily selected, and their minimum inhibitory concentrations (MICs) against Gram-positive bacteria were predicted from the antimicrobial quantitative relationship of plant flavonoids to Gram-positive bacteria. The results showed they have different antimicrobial activities. After their MICs againstStaphylococcus aureuswere determined using the broth microdilution method, nine compounds with MICs ranging from 2 to 4096 μg/mL or more than 1024 μg/mL were eventually selected, and then their MICs againstS. aureuswere determined interfered with different concentrations of menaquinone−4 (MK−4) and the MKs extracted fromS. aureus. The results showed that the greater the antibacterial activities of plant flavonoids were, the more greatly their antibacterial activities decreased along with the increase in the interfering concentrations of MK−4 (from 2 to 256 μg/mL) and the MK extract (from 4 to 512 μg/mL), while those with the MICs equal to or more than 512 μg/mL decreased a little or remained unchanged. In particular, under the interference of MK−4 (256 μg/mL) and the MK extract (512 μg/mL), the MICs ofα-mangostin, a compound with the greatest inhibitory activity toS. aureusout of these twelve plant flavonoids, increased by 16 times and 8 to 16 times, respectively. Based on the above, it was proposed that the quinone pool is a key target of plant flavonoids inhibiting Gram-positive bacteria, and which likely involves multiple mechanisms including some enzyme and non-enzyme inhibitions.