The activation of persulfates to degrade refractory organic pollutants is a hot issue in advanced oxidation right now. Here, it is reported that single-atom Fe-incorporated carbon nitride (Fe-CN-650) can effectively activate peroxymonosulfate (PMS) for sulfamethoxazole (SMX) removal. Through some characterization techniques and DFT calculation, it is proved that Fe single atoms in Fe-CN-650 exist mainly in the form of Fe-N3O1 coordination, and Fe-N3O1 exhibited better affinity for PMS than the traditional Fe-N4 structure. The degradation rate constant of SMX in the Fe-CN-650/PMS system reached 0.472min-1, and 90.80% of SMX can still be effectively degraded within 10min after five consecutive recovery cycles. The radical quenching experiment and electrochemical analysis confirm that the pollutants are mainly degraded by two non-radical pathways through 1O2 and Fe(IV)═O induced at the Fe-N3O1 sites. In addition, the intermediate products of SMX degradation in the Fe-CN-650/PMS system show toxicity attenuation or non-toxicity. This study offers valuable insights into the design of carbon-based single-atom catalysts and provides a potential remediation technology for the optimum activation of PMS to disintegrate organic pollutants.