Introduction: The dynamic positioning system resists the environmental forces such as wind, wave and current acting on the ship through the thruster, so that the ship can remain in the position required by the sea level as much as possible, and the operation is very convenient. But its current dynamic positioning ability can not meet people's needs.Methods: A Kalman filter based on untracked optimization was designed for dynamic positioning control system. Then the intelligent control algorithm is designed for the dynamic positioning top-level controller and thrust optimal distribution controller, which occupy an important position in the system, namely the adaptive weight variation particle swarm optimization algorithm and thrust optimal distribution algorithm.Results and Discussion: The average position error of three degrees of freedom after filter processing is 1.53 m. Compared with other mainstream controllers, the mean root error of controllers based on adaptive weight variation particle swarm optimization in environment A and B is 2.295 and 1.8 m, respectively. In environment C, the controller based on thrust optimization allocation algorithm can get the optimal solution when the full rotary thruster reaches the 7 s and the channel thruster reaches the 4 s. The thrust exclusion zone is crossed at 46 s in environment D. In the dynamic positioning capability curve of the system, the experimental hull can balance the different environmental loads at all angles. In summary, the intelligent control algorithm proposed in this paper can effectively improve the positioning ability of the dynamic positioning control system and meet the needs of people for ship navigation today.