In this paper, a protect system consists of a re-entrant hexagon honeycomb cored sandwich panel and a homogenous steel plate was firstly proposed. The parametric study including boundary conditions, geometric and thickness parameters of the protect system was conducted. It was found that, under the presented set-up, the boundary conditions did not affect the energy absorption of the protect system, they only altered the internal energy distribution among the protect system. Finally, a novel multi-scale optimization was conducted to further improve the performance of the protect system. Another conventional multi-objective optimization was also conducted for comparison. The results showed that, by affording less computational effort, the multi-scale optimization improved the ASEA (areal specific energy absorption) by 4.9% and reduced MaxD (maximum displacement) by 1.8%, comparing to the conventional multi-objective optimization.