We first attempted to fill CuO particles in the channel of carbon nanotubes (CNTs) as novel catalytic materials CuO@CNTs used for ozonation of rhodamine B (RhB) in aqueous solution. Catalyst samples were characterized by transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD), thermogravimetry (TG), the Brunauer-Emmett-Teller (BET) surface area method, X-ray photoelectron spectroscopy (XPS), and Fourier transform IR (FT-IR) method. Removal efficiency of RhB was significantly promoted at the presence of ozonation/CuO@CNTs compared with that of ozonation alone, ozonation/pure CNTs, and ozonation with CuO-coating CNTs catalyst (CuO/CNTs). Electron paramagnetic resonance (EPR) experiments, molecular dynamics (MD) simulation, and density functional theory (DFT) calculations further demonstrated that CNTs provided a confined environment to promote the decomposition of ozone and the generation of hydroxyl radical, making the ozonation process more efficient. This study provided a possible treatment approach for organic pollutants by using CNTs-confined nanocatalysts in aqueous solution.