A cone-beam CT three-dimensional reconstruction method and system. By means of GPU acceleration, while also using geometric symmetry to reduce the calculation amount, a thread is established for each connecting line between pixels and a ray source; the length of the connecting line in each voxel of three-dimensional data is calculated, and then the x-optimal solution is obtained by the iterative method, so as to achieve the aim of efficiently performing three-dimensional reconstruction and greatly improve the calculation efficiency while ensuring the quality of a reconstructed image.