In order to improve the penetration probability of anti-ship missile, the anti-missile capability of ship-to-air missile weapon system is analyzed. The anti-missile model of ship-to-air missile weapon system is established based on the basic principle of graphic analysis, taking the “Standard Missile-2” of “Keelung” class ship-to-air missile as the research object, and the method is improved according to the shortcomings of the method. Through the analysis of the improved model, the anti-missile capability of the “Standard Missile-2” ship-to-air missile is obtained. The results show that the research can provide some reference for the penetration of anti-ship missile.