Potassium permanganate (Mn (VII)) oxidation, a green advanced oxidation technology, is widely used as an in-situ remediation method for groundwater contamination. Based on the complexity of organic substances in aquatic environments, many novel organic components, whose processes and mechanisms affecting the oxidative efficacy of Mn (VII), remain unknown and need to be studied systematically. Therefore, using the reducing macromolecular quercetin as the organic matter, the efficiency and mechanism of quercetin-bound, low-valent Mn enhanced Mn (VII) oxidation of bisphenol A (BPA) were studied. The pH and concentration of quercetin strongly influenced its performance. Under pH 4.0–6.0, quercetin evidently promoted the BPA degradation rate in the Mn (VII)/quercetin (Mn (VII)/Q) system. However, the presence of quercetin had little effect on the degradation efficiency of Mn (VII) at pH ≥ 7.0. This study found that at pH 4.0–5.0, quercetin could act as both a reductant and complexing ligand in the process of BPA oxidation. As a complexing ligand, quercetin stabilized the intermediate states of Mn (III) to form complexes. These stable complexes could efficiently oxidize BPA. While low concentrations of quercetin were insufficient to complex and stabilize Mn (III), Mn (III) was reduced to Mn (II). Mn (II) then reacted with Mn (VII) to form MnO2, enhancing the degradation efficiency of the Mn (VII)/Q system for BPA through its catalytic and oxidative properties. This study provides a better understanding of the degradation of organic pollutants by KMnO4 in groundwater treatment.