The reconfiguration process for shipboard power system (SPS) reroutes the electric power to restore the power supply for vital loads, and is important to improve the shipboard’s survivability and power supply reliability. A multi-objective model for fault restoration of DC zone distribution system is established to maximize numbers of load power supply and minimize times of switch operation. The objective functions of different dimensions are normalized, and these objective functions are integrated by using the analytic hierarchy process (AHP), then the integer programming (IP) method is used to optimize the integrated objective function, and the optimal switch operation sequence is obtained, and the continuance of electricity supply could be ensured as far as possible. Finally, numerical results based on a typical shipboard power system are used to demonstrate the feasibility and effectiveness of the proposed method, and this method and strategy is a good reference for the study on DC power distribution networks.