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Thrust allocation is an important part of the dynamic positioning system of ships, which determines the control inputs of each thruster device from the control law. In order to improve the faults of thrust allocation algorithms efficiently, the concept of group biasing is given and the adaptive strategy of group biasing method is designed. Consequently, the optimizing adaptive thrust allocation algorithm is proposed which bases on the group biasing and optimal methods, and the amplitude of bias can be adjusted adaptively according to thrust force. Applying the algorithm, the dynamic performances of dynamic positioned ships are improved availably, and the fuel consumption and maneuverability are both considered simultaneously. The validity and excellent performances of this algorithm were proved by the simulation results.