We found recently that intrinsic chemiluminescence (CL) could be produced by all 19 chlorophenolic persistent organic pollutants during environmentally friendly advanced oxidation processes. However, the underlying mechanism for the structure-activity relationship (SAR, i.e., the chemical structures and the CL generation) remains unclear. In this study, we found that, for all 19 chlorophenol congeners tested, the CL increased with an increasing number of chlorine atoms in general; and for chlorophenol isomers (such as the 6 trichlorophenols), the CL decreased in the order of meta- > ortho-/para-Cl-substituents with respect to the -OH group of chlorophenols. Further studies showed that not only chlorinated quinoid intermediates but also, more interestingly, chlorinated semiquinone radicals were produced during the degradation of trichlorophenols by the Fenton reagent; and the type and yield of which were determined by the directing effects, hydrogen bonding, and steric hindrance effect of the OH- and/or Cl-substitution groups. More importantly, a good correlation was observed between the formation of these quinoid intermediates and CL generation, which could fully explain the above SAR findings. This represents the first report on the structure-activity relationship study and the critical role of quinoid and semiquinone radical intermediates, which may have broad chemical and environmental implications for future studies on remediation of other halogenated persistent organic pollutants by advanced oxidation processes.