This paper described the use of modified mesoporous molecular sieves to remove clofibric acid through catalytic ozonation. The mesoporous silicate MCM-48 and Cu-substituted MCM-48 (Cu-MCM-48) with different Cu contents were prepared by hydrothermal method in surfactant solutions. The catalyst was characterized by XRD, UV-vis, and XPS, indicating that copper was successfully doped in the framework of three-dimensional MCM-48 and Cu-O-Si linkage was formed in Cu-MCM-48 samples. The SEM and TEM graphs exhibited that the cubic arrays were highly homogeneous and well-ordered. However, high Cu contents destroyed the basic structure of pure MCM-48 and metallic nanometric clusters accumulated on the surface of samples. The degradation and mineralization of clofibric acid (CA) were investigated with the presence of Cu modified MCM-48 (Cu-MCM-48) during ozonation. When the molar ratio of Si/Cu was 60, TOC removal reached 41.1% at 60 min oxidation time. The catalytic mechanism of Cu60-MCM-48 was also investigated by using density functional theory (DFT). The radical quenching experiments revealed that hydroxyl radical ((OH)-O-center dot) and superoxide radical (O-center dot(2)-) were the reactive oxygen species (ROS) for CA degradation. Cu60-MCM-48 showed favorable removal efficiency in the mild acid condition and remained high Lewis acid amount after reactions according to the results of Fourier transformer infrared (FTIR) of adsorbed pyridine. Furthermore, the possible reaction routes including C1-O and C4-Cl bonds destroying and aromatic ring cleavage were proposed by HPLC-MS. 2-hydroxyisobutiric acid was the main intermediate in ozonation process with the presence of Cu60-MCM-48.