In this work, the mechanism of the activation of peroxides by quinones has been investigated through quantum chemical calculations. Hydrogen peroxide (H2O2), peroxomonosulfate (PMS), peracetic acid (PAA), and CH3OOH were chosen as the model peroxides and p-benzoquinone (p-BQ) and tetrachloro-1,4-benzoquinone (TCBQ) as the model quinones. The nucleophilic attack of peroxides can occur on the carbonyl and olefinic carbons of quinones. For p-BQ, the nucleophilic attack of HO2-, CH3OO-, PMS, and PAA might prefer to occur on the carbonyl carbons, which have more positive atomic charges. Then, further transformation could not be induced from the addition of HO2- and CH3OO- to p-BQ. Comparatively, singlet oxygen (1O2) could be generated in the cases of PMS and PAA. For TCBQ, the chlorine atoms cause the olefinic carbons to carry more positive atomic charges, and then, HO2- preferred to add to the olefinic carbons, which might induce the formation of the hydroxyl radical (•OH). The activation of PMS by TCBQ was similar to that by p-BQ, with the kinetical feasibility of 1O2 formation. These findings may provide some theoretical insights into the reaction of peroxides with quinones, especially into the interconnection between the substitutes and the formation of oxygen-centered radicals (e.g., •OH) and 1O2.