Coded aperture cone-beam computed tomography (CBCT) represents a crucial method for acquiring high-fidelity three-dimensional (3D) tomographic images while reducing radiation exposure. However, projections are non-uniformly and discontinuously sampled with the coded apertures placed in front of the x-ray source, leading to very small reconstruction scale and time-intensive iterations. In this study, an alternative approach to reconstruct coded aperture CBCT based on generative adversarial U-net is proposed to effectively and efficiently reconstruct large scale 3D CBCT images. Our method entails predicting complete and uniform projections from incomplete and non-uniform coded projections, enabling the requirement of continuity for the use of analytical algorithms in 3D image reconstruction. This novel technique effectively mitigates the traditional trade-off between image fidelity and computational complexity inherent in conventional coded aperture CBCT reconstruction methods. Our experimental results, conducted using clinical datasets comprising CBCT images from 102 patients at Nanjing Medical University, demonstrate that high-quality CBCT images with voxel dimensions of 400 × 400 × 400 can be reconstructed within 35 s, even when 95% of projections are blocked, yielding images with PSNR values exceeding 25dB and SSIM values surpassing 0.85.