Successful morphology and defect engineering of semiconductors can improve their photocatalytic efficiency by influencing on surface-interface reaction, extending light response and promoting charge carrier separations. This contribution aims to investigate the correlation of CaCu3Ti4O12 synthesized by a molten salt method between its morphology-defect-crystal structure and photocatalytic performance. The effects of salt amount (LiCl) on the morphology tailoring (octahedron, nanorod and polyhedron), defect engineering (V-O and Ti3+) and corresponding photocatalytic activity of CaCu3Ti4O12 towards antibiotic degradation were systematically explored. Interestingly, large amounts of defects were observed in samples, presence of which turns out to be critical to facilitating carrier separation and governing the production of enhanced visible light photoefficiency of as-obtained nanostructures. The defective (oxygen/metal imperfections) octahedron shaped CaCu3Ti4O12 displayed superior photocatalytic performance, almost 24.14 and 19.69 times as high as that of mono-defective (oxygen defects) octahedrons and nanoparticles. The enhancement in photocatalytic performance was attributed to the unique morphologies and effective carrier separations due to local defects. This is the first systematic investigation on the relationship between morphology-defect-photocatalytic performances of CaCu3Ti4O12 nanostructures. Our study shows that a systematic investigation on synthetic conditions during the molten salt preparation can not only be effectively used in morphology and defect control in CaCu3Ti4O12, but it also calls for more research efforts in effective synthesis and defect engineering with other inorganic materials.