Stowage operations in container terminals are an important part of a port's operational system, as the quality of stowage operations will directly affect the efficiency of port loading and discharge operations, and the scheduling of container shipping liners. The intelligent stowage of containers in container ships was studied in this work. A multi-objective integer programming model was constructed with the minimization of container rehandling, yard crane movements, and the sum of weight differences between stacked container pairs as its objective functions, to address the need for intelligent optimization of single bay export container stowage on a ship's deck. This model also satisfies the stability requirements of preliminary stowage plans drawn by shipping companies, and the operational requirements of container terminals. Linear computational methods were then constructed to transform non-linear constraints into linear ones for better AIMMS solution. Through numerous case analyses and systematic tests, it was shown that our system is able to rapidly solve for stowage planning optimization problems with complex preliminary stowage data, thus proving the applicability and effectiveness of this model. In particular, the application of this model will simultaneously address the safety of ship voyages, the transportation quality of shipping containers and other forms of cargo, and the cost efficiency of ship operations. In addition, this model will also contribute to the optimization of loading and discharge processes in container terminals. Therefore, our model has immense practical value for improving port productivity, as it will contribute to the organization of port operations in a rational, orderly and effective manner.