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This paper proposes a new reconfigurable flight control system design methodology using the optimal eigenstructure assignment with constrained output feedback. An integrated performance index is given in this methodology which combines the performance index of the reconfigured eigenstructure and the performance index of the stability of the reconfigured closed-loop system. Then particle swarm optimization algorithm is utilized to minimize the integrated performance index to obtain the optimal feedback gain. In view of an impaired lateral flight control system with the sideslip angle sensor and the aileron are all in complete failure, an illustrative design example using the proposed methodology to design the reconfigurable flight control system. Simulation results are provided to show the effectiveness and the superiority of the proposed methodology.