In establishing the kinetics, energetics and mechanisms of phenolic degradation reactivity, active reactive oxygen species (ROS) on catalysts surface could exert a vital part. This paper attempts to account for different ROS at the atomic level using octahedral layered birnessite-type MnO2 as a platform with different crystal planes which could induce the Jahn-Teller effect and further realize deep mineralization of phenolic pollutants at low temperature. The catalytic degradation phenol rate of (100) MnO2 is 3 times as much as that of (001) MnO2, and the activation energy of the catalytic reaction is reduced by 11 KJ/mol. The degradation content of (100) MnO2 surpasses 30% than that of (001) MnO2. Both spin-trapping EPR and DFT results show superoxide ([rad]O2−) species could exist on (001) MnO2 through one electron transfer, while the peroxide (O22−) species exist on (100) MnO2 via two electrons transfer. All the results illustrate that birnessite MnO2 possesses surface-dependent molecular oxygen activation properties.