To research the effect of coordinated anti-ship operation of ARM and conventional missile, established the model of missile penetration probability. The damage models of search radar, guidance radar and gun pointing radar with ARM are created based on the research on the damage probability of ARM to anti-air radar. The damage effects of ARM in different situation are simulated. And in the case of certain total of the missiles, the optimized model used in coordinated anti-ship operation of ARM and conventional missile is simulated and analyzed. The simulate results demonstrated that the optimization way can reduce the capability of detection and strike, and increase the penetration probability and the capability of anti-ship.