Abstract: In order to improve the penetration capability of middle-range/long-range ballistic missile in middle flight stage, the menaces for ballistic missile and the measures of penetration at present were analyzed. Meanwhile, the limitations of procedural penetration strategy and the advantages of intelligent penetration strategy were pointed out. By analyzing ground-based midcourse defense system and the operating mode of its interception subsystem as well as spectral signature, infrared (IR) warning system was innovatively installed on the warhead of penetration missile. According to the characteristics of Exoatompropheric Kill Vehicle (EKV) and its booster rocket, the method of smart penetration was proposed, which used Ballistic Missile-borne (BM-borne) IR detection system to detect EKV. Based on analysis and computation of the performance parameters of BM-borne IR detection system: field of view, operating distance, warning time and sense spectrum ranges for example, the conclusion that the method of smart penetration is feasible can be drawn.