Fault reconfiguration of shipboard power system is viewed as a typical nonlinear and multi-objective combinatorial optimization problem. A comprehensive reconfiguration model is presented in this paper, in which the restored loads, switch frequency and generator efficiency are taken into account. In this model, analytic hierarchy process (AHP) is proposed to determine the coefficients of these objective functions. Meanwhile, a quantum differential evolution algorithm with triple quantum bit code is proposed. This algorithm aiming at the characteristics of shipboard power system is different from the normal quantum bit representation. The individual polymorphic expression is realized, and the convergence performance can be further enhanced in combination with the global parallel search capacity of differential evolution algorithm and the superposition properties of quantum theory. The local optimum can be avoided by dynamic rotation gate. The validity of algorithm and model is verified by the simulation examples. © 2016, Shanghai Jiaotong University and Springer-Verlag Berlin Heidelberg.