The permutation algorithm with simulated annealing is proposed for the laser antimissile problem. The attacking sequence optimization plays an important role in the real-time laser antimissile problem. When faced with many targets, it is clearly essential for the laser antimissile system to determine the sequence of the attacking targets. In order to maximize attacking targets are destroyed. This paper presents a permutation algorithm based on the simulated annealing method. The permutation algorithm includes of two exchange strategies which are adjacent exchange and symmetric exchange. Finally, taking ten targets as an example, the simulation results show that the proposed algorithm has better solution than that of pure permutation algorithm and this achievement can be used in the real application.