This paper compares the penetration capabilities of the same type anti-ship missiles with millimeter wave (MMW) seeker and centimeter wave seeker, and constructs mathematical models of penetration probability and saturation attack number for all anti-ship missiles used in the countermeasure system, according to the rule which makes the ship-borne air defence system oppase as far as possible and equally, and combining the actual combat situation. It can be seen, from analysis of the countermeasure process between anti-ship missile and surface naval ship, that for the same type of anti-ship missile with different seekers, the main influence on the penetration capability is from electronic jamming system. Based on the built model, the penetration capabilities of the same type anti-ship missiles with MMW and centimeter wave seekers are simulated. The simulated results show that the penetration capability of MMW seeker is slightly better than that of the centimeter wave seeker and its saturation attack number is also influenced by the discovering probability greatly. Finally, some suggestions to get superior penetration effect are given for a commander to choose seeker type suitably.