Spinel nanomaterials, as magnetic catalysts for catalytic ozonation, have gradually attracted the attention of researchers due to the easy-to-separate and recyclable properties. However, few studies have systematically studied the catalytic mechanism. Hence, normal spinel-ZnFe2O4 and inverse spinel-MnFe2O4 were prepared and applied to catalyze the ozonation of oxalic acid (OA) and phenol in this study. ZnFe2O4 and MnFe2O4 showed opposite catalytic abilities: MnFe2O4 performed better than ZnFe2O4 in OA decomposition and the TOC (total organic carbon) removal efficiency reached 92.1%; ZnFe2O4 performed better than MnFe2O4 in phenol decomposition and the TOC removal efficiency reached 60.3%. Radical quantitative results showed •OH and •O2– were the main radicals with MnFe2O4 during the catalytic ozonation, and •OH was the main radical for the ZnFe2O4. DFT (density functional theory) calculation and catalysts characterization indicated a smaller band gap endowed MnFe2O4 with higher electron transport capacity than ZnFe2O4, which catalyze ozone decomposition into •O2–; ZnFe2O4 possessed more abundant surface hydroxyl groups than MnFe2O4, which catalyze ozone decomposition into •OH. Conclusively, this study systematically revealed the different catalytic mechanisms of normal spinel-ZnFe2O4 and inverse spinel-MnFe2O4, and showed a positive effect on the application of spinel catalysts.