In order to improve the anti-damage capability of the modern submarines, this paper used multi-material ALE algorithm of LS-DYNA software to conduct the simulation test analysis of shaped charge warhead penetrating water medium armor. Based on damage mechanism of the torpedo, material models and equations of state (EOS) were defined. And then the fitting curve of the maximum node velocity on the propagation path of the penetration head was given. The problem of computing instability often appearing in simulation test also was solved. The simulation results showed that the designed warhead can meet check request, and can afford reference for the evaluation of shaped charge warhead damage power and simulate targets design of submarine.