This study systematically compared the effect of microwave irradiation activated persulfate (MW/PS) and hydrogen peroxide (MW/H2O2) on organic matter removal in mature landfill leachate effluent from a membrane bioreactor (MBR), the reactive oxygen species (ROS) produced, and the degradation and transformation mechanisms of organic substances. An obvious synergistic effect was identified in the MW/PS and MW/H2O2 processes. The synergistic effect of the MW and PS (synergy coefficient F = 23.67) was significantly higher than that of the MW and H2O2 (synergy coefficient F = 11.43). The MW/PS process had a stronger degradation effect on organic substances than the MW/ H2O2 process, even when the PS dosage was significantly lower than the H2O2 dosage. The removal rate and kobs (initial reaction rate) of the two processes could be raised by increasing the oxidant dosage. Increasing the MW output power improved the removal rate of organics by the two processes, but an excessive MW output power only improved the kobs of the two processes, while the effect on organic matter removal was not significant. The MW/H2O2 process only removed organics expeditiously under acidic conditions, while the MW/PS process resulted in a strong degradation of organic matter under a wide range of pH values. A quenching experiment using alcohols indicated that both SO4•- and •OH existed in the MW/PS process, with SO4•- playing a leading role in the degradation of organics, while •OH played a leading role in the MW/H2O2 process. A spectrum analysis based on the quenching experiment demonstrated that the two processes destroyed the characteristic structure of humus and refractory organics in the leachate (i.e., humic acid-like (HAL) and fulvic acid-like (FAL) substances), mainly through the free radical oxidation mechanism. The SO4•- degraded HAL substances efficiently, while •OH had a better degradation effect on FAL substances. Therefore, the MW/PS process had a stronger degradation effect on organics than the MW/H2O2 process due to the enhancement of ROS production. The final energy consumption analysis revealed that the energy conserved by the MW/PS process was about 614.2 kWh per unit volume of effluent compared to the MW/H2O2 process. This study provides a useful reference for the use of the MW/PS and MW/H2O2 processes to eliminate refractory organics in leachate effluent from an MBR.