In order to reduce the light weight and improve the economy, the weight reduction of hatch cover structure of a ship is studied. The Latin square test method is used to establish the sample space, and the finite element model is used to find the solution according to the sample parameters. The response surface model method is used to establish the approximate model of hatch cover structure design, the requirements of stress and deformation in the specification are taken as the design constraints, and the optimization design of hatch cover structure of a ship is made based on the multi-island genetic algorithm. The results show that the optimization solution is of good convergence and can meet the specification requirements.