Abstract Cellular automata transform (CAT) based watermarking method can provide multi-transform planes for embedding watermark. In this paper, to overcome conventional transform-based watermarking methods have only one transform plane for watermark embedding, we propose a CAT-based watermarking system, in which the three-dimensional (3-D) watermark data is decomposed by the computational integral imaging (CII) technique and be embedded into the CAT domain. However, in the 3-D watermark reconstruction process, the computational integral imaging reconstruction (CIIR) technique in CII system that can degrade the quality of the extracted watermark due to the pixel overlapping. We introduce the super-resolution reconstruction technique that can effectively improve this problem. Some experiments are carried out to verify the performance of the CAT-based watermarking scheme. From the experimental results, the proposed watermarking system can provide good imperceptibility and high robustness.