In this new era of the army with goals to reduce manning and increase system survivability, automatic reconfiguration of the electrical network in a shipboard power system(SPS) is critical for quickly restoring service to a section of the power system to survive battle damage. In this paper, according to the characteristics of SPS, a new system structure description matrix-enlarged associated matrix is built, which is convenient for system calculation and topology identification of SPS fault system. Combing the enlarged associated matrix, an intelligent reconfiguration methodology is presented, which using accelerated genetic algorithm, adding the new operators, such as annealing selection based on energy-entropy, immune selection and vaccination. RTDS fault restoration experiments show that the intelligent network reconfiguration algorithm can improve speed of convergence and precision of reconfiguration, while satisfying the operational requirements and priorities of loads.