Metal oxide nanocomposites with photocatalytic activity have the potential for many applications in environmental remediation and biomedicine. In this study, we investigated the formation and stabilization of electrons/holes from three metal oxide–silica nanocomposites (CuO–SiO2, Fe2O3–SiO2 and ZnO–SiO2) under irradiation by electron paramagnetic resonance (EPR) technology. The characteristic EPR signals with g=2.00070–2.00105, ΔHp-p=2.17–2.37G were determined, which corresponded to lattice-trapped electrons. Moreover, the generation of active species from CuO–SiO2, Fe2O3–SiO2 and ZnO–SiO2 in aqueous solution under irradiation was also systematically studied. The results showed that all the three nanocomposites could generate hydroxyl radical, singlet oxygen and electron. CuO–SiO2 was more effective than Fe2O3–SiO2 and ZnO–SiO2 in producing hydroxyl radical and electrons, while ZnO–SiO2 was the most efficient in generating singlet oxygen. In addition, CuO–SiO2 exhibited most obviously photocatalytic activity toward degradation of bisphenol A, followed by Fe2O3–SiO2 and ZnO–SiO2. These findings will provide vital insights into photocatalytic mechanisms and potentially photoinduced toxicity of metal oxide–silica nanocomposites.