A structure optimization for the initial design stage using FEM of ship is under consideration in this paper. General bulk carrier is selected for the object of the optimization. Shapes of the bottom structure of ship are taken as design variables. Since the design variables affect the shape of structure, FEM model should be updated during the optimization. Moreover the structure of ship is so large and complicated that make shape optimization of ship structure very difficult. Individual mesh-subdivision technique and multi-point constraint method are introduced for making this optimization possible. However, creating FEM data sets for them requires a lot of manpower. In order to remove this drawback, PrimeShip-Hull is used since it has a function recognizing structure members of ship. A FEM data set which can be applied individual mesh-subdivision technique and multi-point constraint method is made from structure members of PrimeShip-Hull automatically. Five design variables for shape optimization of double bottom structure of ship are considered here and a numerical example is shown.