Single-atom catalysts (SACs) have been widely recognized as state-of-the-art catalysts in environment remediation because of their exceptional performance, 100% metal atomic utilization, almost no secondary pollution, and robust structures. Most recently, the activation of persulfate with carbon-based SACs in advanced oxidation processes (AOPs) raises tremendous interest in the degradation of emerging contaminants in wastewater, owning to its efficient and versatile reactive oxidant species (ROS) generation. However, the comprehensive and critical review unraveling the underlying relationship between structures of carbon-based SACs and the corresponding generated ROS is still rare. Herein, we systematically summarize the fundamental understandings and intrinsic mechanisms between single metal atom active sites and produced ROS during AOPs. The types of emerging contaminants are firstly elaborated, presenting the prior pollutants that need to be degraded. Then, the preparation and characterization methods of carbon-based SACs are overviewed. The underlying material structure–ROS type relationship in persulfate-based AOPs is discussed in depth to expound the catalytic mechanisms. Finally, we briefly conclude the current development of carbon-based SACs in AOPs and propose the prospects for rational design and synthesis of carbon-based SACs with on-demand catalytic performances in AOPs in future research.