In this paper, a three-dimensional (3D) image security system combines the use of the smart pixel mapping (SPM) algorithm and the Fibonacci transformation technique is proposed. In order to reconstruct orthoscopic 3D images with improved image quality, a smart pixel mapping process is adopted. Based on the SPM-based computational integral imaging (CII) system, the depth-converted elemental image array (EIA) is obtained for increasing the quality of the reconstructed image. In the encryption process, the depth-converted EIA is scrambled by the Fibonacci transformation (FT) algorithm. Meanwhile, the computational integral imaging reconstruction (CIIR) technique is used to reconstruct the 3D image in the image reconstruction process. Compared with conventional CII-based 3D image encryption methods, the proposed method enable us to reconstruct high-resolution orthoscopic 3D images at long distance. To demonstrate the effectiveness of the proposed method, some numerical experiments are made to test the validity and the capability of the proposed 3D image security system.