Widely distributed manganese oxides are among the strongest oxidants in nature and effectively enhance the water decontamination by peracetic acid (PAA) activation. However, the precise mechanism requires further investigation. In this work, the intrinsic mechanism of PAA activation by MnO2 was systematically studied. Through in situ diffuse-reflectance UV–vis spectra and resonance Raman spectra, the active species was identified as a non-radical heterogenous Mn(III)-hydroperoxo complex. During the process, PAA drastically converted Mn(IV) in MnO2 into homogeneous Mn(II), which subsequently generated the active Mn(III) species in the aid of PAA on the surface of MnO2. By interacting with pollutants, the peroxide bond in Mn(III)-hydroperoxo broke, accompanied by the regeneration of Mn(IV). Eight phenolic compounds having para-substituent of –CH3, −H, −Cl, –COCH3, –CHO, –COOH, –COOCH3, and –NO2 were selected for degradation. Due to the electrophilic character of Mn(III)-hydroperoxo, the removal rates were 100 %, 100 %, 98.8 %, 69.8 %, 49.6 %, 30.2 %, 28.1 %, and 3.0 % respectively at the 45 min of experiment. The MnO2/PAA system was also readily coupled with a filtration membrane for continuous treatment of phenol in nearly 100 % removal efficiency. This study not only offered an efficient non-radical PAA activation protocol for water decontamination, but also elucidated the catalytic mechanism and redox cycle of MnO2 in PAA solution in the selective oxidation process.