Iterative image reconstruction (IIR) with sparsity-exploiting methods, such as total variation (TV) minimization, claims potentially large reductions in sampling requirements. However, the computation complexity becomes a heavy burden, especially in 3D reconstruction situations. In order to improve the performance for iterative reconstruction, an efficient IIR algorithm for cone-beam computed tomography (CBCT) with GPU implementation has been proposed in this paper. In the first place, an algorithm based on alternating direction total variation using local linearization and proximity technique is proposed for CBCT reconstruction. The applied proximal technique avoids the horrible pseudoinverse computation of big matrix which makes the proposed algorithm applicable and efficient for CBCT imaging. The iteration for this algorithm is simple but convergent. The simulation and real CT data reconstruction results indicate that the proposed algorithm is both fast and accurate. The GPU implementation shows an excellent acceleration ratio of more than 100 compared with CPU computation without losing numerical accuracy. The runtime for the new 3D algorithm is about 6.8 seconds per loop with the image size of 256×256×256 and 36 projections of the size of 512×512.