The penetration of projectiles into targets has a broad background in engineering. In this work, numerical simulations of the projectile-target penetration problem are conducted using the Finite Element Method (FEM), the Smoothed Particle Hydrodynamics (SPH) and the Finite Element–Smoothed Particle Hydrodynamics Adaptive Coupling Method (FE-SPH ACM) based on the LS-DYNA software package. First, the penetration experiments using aluminum targets and ceramic targets are simulated. The experimental and simulation results show that the FE-SPH ACM has the better accuracy in calculating the debris cloud head velocity and interface velocity, with an error of no more than 4%. Furthermore, we use the FE-SPH ACM to investigate the anti-penetration performance of aluminum/ceramic composite targets in different combinations. We find that the reasonable layout can improve the protective performance of multi-layered target, especially composite target plates with ceramic as the front layer. In addition, the ballistic limit velocities for ceramic-aluminum ratios of 3/7, 5/5 and 7/3 are approximately 1300 m/s, 1400 m/s and 1500 m/s, respectively. Obviously, increasing the proportion of ceramic materials can enhance the anti-penetration performance.