The effect of different crystal phases, i.e. spinel phase (CuMn2O4) and amorphous phase (Cu0.2MnOx), was explored in Cu-Mn catalytic ozonation of toluene. The toluene removal efficiency followed the order of Cu0.2MnOx (91.2%) ˃ CuMn2O4 (74.5%) ˃ commercial catalyst Cu0.3MnOx (70.3%) in 130 min, and the higher CO2 yield (67.6%) could be also observed using Cu0.2MnOx. In order to investigate the effect of phases on the toluene degradation pathway, the intermediates and byproducts were identified by DRIFTS, GC-MS, and TOF-SIMS. No obvious difference was observed in the distribution of byproducts, except for the quantities, suggesting the discrepancy of oxidation rate. On the other hand, the catalysts were characterized before and after the ozonation process by TEM, BET, XPS, XRD, EPR, TGA, and TPR. It was proposed that for amorphous catalysts, the oxygen vacancy (Vo) helped the chemisorption of toluene, and adjacent Mn reacted as the main active site for the ozonation process. While, the redox pair of Cu+/Mn4+ and Cu2+/(Mn3+, Mn2+) in the spinel phase plays an important role in the generation of oxygen vacancies for O3 decomposition.