The genetic algorithm based on permutation distance definition is used to solve the laser antimissile system. When faced with multiple attacking targets, it is clearly important for the laser antimissile system to determine the sequence of the attacking targets to be intercepted so that the maximum attacking targets are destroyed. It’s very difficult to find the global optimal solution, especially when the number of the targets is greater than six. The permutation distance definition is introduced to measure the distribution of the population. The successive zeros permutation distance is to stop the genetic algorithm iterations. Finally, taking ten targets as an example, the simulation results show that the convergence of the algorithm is fast and this achievement can be used in the real application.