The layout design of component plays an important role in the design and usability of many engineering products. The Engineering artifacts of today are becoming increasingly complicated. The simulated annealing method has been applied effectively to the layout and packing problems of wafer. The main characteristics of simulated annealing method is that an optimum can be obtained from the many local optimums by controlling the temperature and introducing the statistic flickering. The objective of this study is to suggest a method to apply the simulated annealing method to the three dimensional layout design of submergible boat which has multiple constraint conditions and evaluation criteria. We describe an approach to define cost function, constraints and generate layouts using a computer. In this research three dimensional LAYout Design Optimization Program(LAYDOP ver.2) has been developed. The layout result(the total value of evaluation criteria) designed by a human layout expert has been improved by 31.0% using this program.