In this paper, we present a non-linear integer programming by genetic algorithm (GA) for available sizes of stiffener or thickness of plate in a job site. GA can rapidly search for the approximate global optimum under complicated design environment such as ship. Meanwhile it can handle the optimization problem involving discrete design variable. However, there are many parameters have to be set for GA, which greatly affect the accuracy and calculation time of optimum solution. The setting process is hard for users, and there are no rules to decide these parameters. In order to overcome these demerits, the optimization for these parameters has been also conducted using GA itself. Also it is proved that the parameters are optimal values by the trial function. Finally, we applied this method to compass deck of ship where the vibration problem is frequently occurred to verify the validity and usefulness of nonlinear integer programming.