The work aims to propose a method to optimize the layout of products on pallets and the layout of pallets and products in containers to maximize container space utilization, thus solving the problem in pallet packing and container loading of factory products. A mixed integer programming model was developed to optimize the volume of the loaded product under realistic constraints. Due to the complexity of the problem, the studied problem was divided into two sub-problems and a two-stage loading model was established for solution. In the first stage, a two-dimensional container loading model was established to determine the plane layout of pallets on the bottom of containers. In the second stage, a three-dimensional pallet loading model was established to determine the 3D layout of products on the pallet. In view of that accurate solution was time-consuming, a two-stage heuristic algorithm was designed to solve the two sub-problems. To verify the effectiveness of the model and algorithm, two groups of examples with different sizes were adopted. The results showed that the average difference of loading rate was 0 and −0.5% in small and large-scale experimental cases, respectively, but the calculation time was quite different. The model and algorithm proposed could obtain the optimal solution or approximate optimal solution in a reasonable time. This study can provide a fast and efficient solution for pallet packing and container loading of factory products.