Pallets are an important transportation tool in modern shipbuilding. With shipbuilding now trending towards larger ships, empty pallet allocation needs to meet the demands of having low costs and being sustainable for green shipbuilding. Thus, with the development of a pallet pool system, a new shipbuilding empty pallet pool allocation (SEPPA) pattern is proposed in this study. An integrated framework is developed that combines a mathematical planning model for a SEPPA pattern with a green allocation strategy. For the base case, the operation costs of the traditional shipbuilding empty pallet allocation (TSEPA) pattern and the SEPPA pattern are solved by applying an improved genetic algorithm for different pallet supply and demand situations. The results show that the SEPPA pattern is more cost-efficient than the TSEPA pattern. With increasing imbalances between supply and demand, the operation costs of the SEPPA pattern are lower than that of the TSEPA pattern. In general, the distribution of supply and demand will affect operation costs. Reasonable safety inventory intervals can reduce the operation costs of empty pallet allocation. This research may support decision making by shipbuilding pallet managers as they seek to minimize the costs of their pallet operations, by adopting practices and adapting strategies for their specific conditions.