Peroxymonosulfate (PMS)-based advanced oxidation processes (PMS-AOPs) as an efficient strategy for organic degradation are highly dependent on catalyst design and structured active sites. However, the identification of the active sites and their relationship with reaction mechanisms for organic degradation are not fully understood for a composite catalyst due to the complex structure. Herein, we developed a family of Co encapsulated in Ndoped carbons (Co-PCN) with tailored types and contents of active sites via manipulated pyrolysis for PMS activation and ciprofloxacin (CIP) degradation, focusing on the correlation of active sites to generated reactive species and degradation routes of organics. The structure−function relationships between the different active sites in Co-PCN catalysts and reactive oxygen species (ROS), as well as bond breaking position of CIP, were revealed through regression analysis and density functional theory calculation. Co−N x , O−CO, CO, graphitic N, and defects in Co-PCN stimulate the generation of 1 O 2 for oxidizing the C−C bond in the piperazine ring of CIP into CO. The substitution of F by OH and hydroxylation of the piperazine ring might be induced by SO 4•− and • OH, whose formation was affected by C−O, Co(0), Co−N x , graphitic N, and defects. The findings provided new insights into reaction mechanisms in PMS-AOP systems and rational design of catalysts for ROS-oriented degradation of pollutants.