The paper aimed to analyze the dynamic response of a new type penetrating missile in rotary attacking warship. The dynamic response characteristics of the penetrator become more complex when attacking the ship target due to the special materials of the deck such as stiffeners. Therefore, different from attacking other targets, the article reveals the design rules of precession penetration ammunition and fuze. A physical model of the missile target is established to study the numerical simulation of the penetration process of rotating projectile into a stiffened target based on finite element analysis (FEA) software. We studied the dynamic response characteristics of different projectile positions, rotational speeds, and positions that act in precession penetration. As experimental results show, the residual velocity of the precession penetrator decreases with the distance between the projectile point and stiffener. When the projectile penetrates the second target plate, the acceleration is greater than that in the first layer. It is proved that the deflection angle of the shell body is affected by comprehensive factors. The rotational speed in the projectile has less contribution to precession penetration ammunition. In addition, the change of acceleration in the missile’s central section can be significantly perceived in the direction perpendicular to the penetration direction.