The thrust allocation of a ship dynamic positioning system allocates the control force to thrusters by calculating thrust and angle of each thruster. Under extreme sea environment such as gust, the output value of control force is usually beyond the ability of thrusters resulting in the fault of thrust allocation. To solve this problem, a method of reducing all the generalized forces with the same scale factor which is obtained based on multiobjective optimization is proposed in this paper. Simulation results show that the proposed thrust allocation method is efficient in extreme sea environment.