When the anti-ship missile is attacked by the enemy's anti-aircraft missile, in order to compare the penetration effect of the anti-ship missile with snake maneuver and without end maneuver, the model of the anti-ship missile against the ship-to-air missile is established. In the background of interception and confrontation, the model considers the influence of many factors on the anti-ship missile, including interference, modeling error, sea condition, uncertainty, etc. At the same time, it also considers the forward angle constraint and dead zone constraint of the ship-to-air missile. Based on this model, the terminal penetration trajectory of anti-ship missile is simulated under different interception conditions. The simulation results show that the penetration effect of the anti-ship missile with longitudinal snake-like maneuver is the best, followed by the anti-ship missile with heading snake-like maneuver, and the penetration effect of the anti-ship missile without terminal maneuver is the worst.