Aerobic granular sludge membrane bioreactors (AGMBRs) are a viable option for municipal sewage reuse; however, the issue of membrane fouling remains a significant obstacle to overcome to achieve large-scale implementation. Therefore, a novel thermal/Fe2+/persulfate (PDS) system was proposed to investigate its alleviation effect on membrane fouling in AGMBR. The findings indicated that the thermal/Fe2+/PDS system demonstrated superior efficacy in eliminating pollutants from raw sewage. Radical scavenging experiments demonstrated that sulfate radicals and coagulation were the primary contributors to mitigating membrane fouling in the thermal/Fe2+/PDS system, effectively reducing fouling resistance and retarding the decline in membrane flux. Analysis of interfacial interaction energy indicated that increasing the electrostatic double-layer repulsion between foulant–membrane and foulant–foulant could mitigate membrane fouling. Additionally, the interfacial characteristics (membrane surface morphology and foulant content) of the fouled membranes were characterized to further validate the efficacy of this system in alleviating membrane fouling. The correlation analysis revealed a positive association between the mitigation of membrane fouling and the substantial elimination of various pollutants, such as chemical oxygen demand, polysaccharides, and suspended solids. This study highlights the exceptional performance of the thermal/Fe2+/PDS system and provides novel insights into alleviating AGMBR membrane fouling.