HPS (Honeycomb-like Protective Structure) is a newly proposed protective structure filled with sandy soil. In order to investigate the penetration resistance of the structure, numerical simulations based on SPH method had been carried out by using LS-DYNA, which are corresponding to the experiments. The calibrated model leads to reasonable predictions of the dynamic responses and damage modes of the HPS. More situations were carried out taking factors influencing the penetration into consideration, including point of impact, angle of impact, and projectile caliber. Penetration mode was established by analyzing the energy dissipation and investigating the mechanism from the phenomenological viewpoint. Simulation results show that the resisting forces and the torque that act on the long rod projectile would be greater than those acting on the short one when instability occurred. Besides, approximate 45 ∘ angle of impact was formed in the case of off-axis, which has a certain influence on the ballistic stability, resulting in more kinetic energy of projectile dissipating in HPS and less depth of penetration. The kinetic energy of projectile dissipated in sandy soil largely and the strip slightly, and the former was greater than the sum of the latter.