Sandwich structure is one of the blasts protecting and energy absorbing materials with different types of light weight cores. This article aimed at investigating blast response of hexagonal honeycomb sandwich structure having perforations along the cell height of core over conventional honeycomb cores. The study discussed the mechanics of deformation behavior of perforated sandwich structure to improve the energy absorption characteristics of the bare honeycomb core sandwich structure. Detailed numerical analysis is conducted to accurately produce the deformation process with finite element analysis using explicit software LS-DYNA®. Blast load resulting from 1 kg TNT on the sandwich structure is applied using Conventional Weapons Effects Program (ConWep) function available in LS-DYNA. Several different parameters consisting of varying sizes of perforation by changing d/l ratio, shape, number of perforations and different facesheet and backsheet thicknesses, and different scaled distances are investigated in detail. The results indicated that both size and shape and number of perforations have significant influence on reduction of blast impulse. The variation of facesheet and backsheet thicknesses without changing the overall thickness of the structure also has evident effect in blast resistance capability of perforated honeycomb sandwich structure. The blast mitigation and energy absorption capacity of honeycomb core sandwich structure can be improved with the provision of perforations and optimizing the arrangement of holes. The perforated honeycomb core is further investigated based on analytical formulation developed using single degree of freedom (SDOF) system analysis approach. Optimization study is done further to get the best configuration based on different design variable limits.