In this paper, a method to apply the simulated annealing method to three dimensional layout design problem which has multiple constraint conditions and evaluation criteria, was suggested. A program to support three dimensional layout design was developed according to the suggested method. This program was applied to the layout design of the wireless unmaned ocean space submergible boat. The layout result was improved 19.0% for the result of layout design expert. By this, it was verified that the suggested method has validity in supporting three dimensional layout design problem.