The paper aims to develop a non-standard pallet size optimization design system to improve logistics efficiency and reduce logistics cost. The plane utilization rate of goods loaded on pallets and the space utilization rate of transportation vehicles are used for double constraints. The stacking is carried out in four ways:simple overlap, positive and negative interleaving, crisscross and rotation interleaving. The optimization algorithm is constructed with the highest loading volume of a single vehicle as the optimization objective. On this basis, the optimization design system is designed and verified by a numerical example. According to the calculation of the given premise data, the optimal pallet size is 1 200 mm×1 029 mm, and the corresponding loading mode is positive and negative interleaving. The system has a certain practical value, but there are still some problems, such as the shape of the objects to be stacked and the way of stacking, and there is room for further improvement.