Manganese dioxide (MnO2) is popular in eliminating organic pollutants in water. The application of chelating agents to enhance the reactivity of MnO2 has been previously reported. Much attention has been taken to increase the amount of Mn(III) species in the manganese oxide/ligands system to achieve a higher degradation. However, the role of Mn2+ is rarely studied. In this study, the efficiency and mechanism of bisphenol A (BPA) degradation by pyrophosphate (PP)-assisted MnO2 in the presence of Mn2+ was investigated. The results show that 25 μM of BPA can be completely removed by the MnO2/PP/Mn2+ system in 90 min. Increasing PP and Mn2+ concentrations effectively improved the degradation of BPA. The primary reactive species for the degradation of BPA was determined to be the Mn(III)-PP complex. Moreover, Mn2+ were verified to play the bridging, reductive, and catalytic roles to enhance the degradation of BPA. Furthermore, the substituted ligands such as nitrilotriacetic acid (NTA) and ethylenediaminetetraacetic acid disodium salt hydrate (EDTA) were verified to exhibit higher activity than citrate on MnO2 activation in the presence of Mn2+. The adaptability of the proposed system was evaluated in various conditions such as the presence of metal cations or inorganic ions and wide solution pH range. In addition, the performance of MnO2/PP/Mn2+ system on BPA removal in the sewage treatment plant outlet water was evaluated as well. These findings highlight the positive role of Mn2+ in the system of MnO2/ligands and provide a practical reference for the application of ligands-assisted manganese oxides in wastewater treatment.