In this paper, a new analysis method for optimization of ship’s comprehensive hydrodynamic performance in complicated operating conditions is proposed. The function of ship’s comprehensive hydrodynamic performance is expressed as a weighted sum of the normalized functions of resistance and propulsion, maneuverability and seakeeping performances. The best comprehensive performance is obtained while the objective function gets maximum with all the constraints satisfied. By adjusting the weight value, any combinations of the functions for resistance and propulsion, maneuverability and seakeeping performances can be achieved. By applying a single-factor sensitivity analysis, the optimized results can be used to find the sensitive variables to help determining the ship geometry and kinematics parameters. This method can help to evaluate the design scheme and improve the ship design efficiency.