Heterogeneous advanced oxidation processes (AOPs) over nanostructured catalysts have been developed as a potential technique for wastewater treatment with the advantages, including high performance, wide operational pH range, and low chemical dosage. However, the surface reaction process and the correlation of catalyst properties and catalytic performance still need to be clarified. In this perspective, we overviewed the heterogeneous catalytic reaction steps of AOPs and summarized the monitoring of catalytic process with molecule-scale insights, and proposed the future challenges and research focuses.