Based on using the normalized sensitivity analysis method to make a necessary choice about numerous design variables of a whole-ship structure, we establish a whole-ship structural optimization model. Under satisfying the condition of frequency, strength, displacement and geometric dimension constraints, the optimization model is expected to achieve the goal of the whole-ship structure weight minimization by optimization of the thickness of plate and model number of stiffener. We use the adaptive simulated annealing algorithm integrated in iSIGHT to analyze an optimization problem of a cutter suction dredger under static and dynamic condition. The optimal result shows: based on meeting the requirements of strength and rigidity, the optimal structure not only reaches a significant decreasing structural mass, but a higher natural frequency reserve, lower vibration level, and finally realizes the whole-ship optimal design.