In order to ensure that the main electric propulsion power system do not lose power for the shipboard power system under fault condition, the shipboard power system topology reconfiguration method is studied. Based on the intelligent agent theory, a kind of all agent based reconfiguration method is established. This method is composed of intelligent environment perception, belief generator, target control and the particle swarm optimal decision. Reconfiguration strategies are used to ensure the uninterrupted power supply, minimization of the shipboard power system loss and maximum of relay protection efficiency, etc. The simulation for a certain type power grid of electric propulsion shipboard distribution system under the three-phase short circuit conditions is conducted. Compared with the particle swarm particle algorithm and genetic algorithm from the simulation result, it shows that the proposed method can ensure the safety operation of the shipboard power system and also has the benefit of less power loss and higher switch efficient under power system fault condition. It can further improve the safety and reliability for shipboard power system.