Emerging single atom catalysts (SACs), especially carbon-based SACs are appealing materials in environmental catalysis because of their ultrahigh performances, environmental friendliness, structural/chemical robustness, and the maximum utilization of active metal sites. The metal centres, carbon matrixes, and coordination characteristics collectively determine the electronic features of carbon-based SACs, and their behaviours in catalysing peroxide activation and efficiencies in advanced oxidation processes (AOPs). However, there is lack of a comprehensive and critical review reporting the successful marriage of carbon-based SACs in AOP-based remediation technologies. It is particularly necessary to systematically compare and reveal the catalytic sites and the associated mechanisms of carbon-based SACs in diverse AOP systems. In this review, we highlight the synthetic strategies, characterisation, and computation of carbon-based SACs, and for the first time, showcase their innovative applications in AOP technologies. We unveil the origins of versatile catalytic oxidation pathways in different AOP systems and the mechanisms of micropollutant degradation over carbon-based SACs, distinguished from the upsized counterparts (metals/oxides and carbon substrates). We also provide directions to the rational design of on-demand SACs for green chemistry and environmental sustainability. Also, we suggest a designated and integrated experimental/theoretical protocol for revealing the structure-catalysis relations of SACs in AOP applications, and propose the prospects for future opportunities and challenges.