For a product packaging system with honeycomb paperboard, its impact resistance caused by drop impact behavior had been concerned. However, irregular hexagon structure of the paper honeycomb core exists in package business, which is attributable to laggard glue applicator. It has an impact on its impact characteristics. Drop impact behavior of packaging system with irregular honeycomb core has been put forward to know its influence. First, on the basis of theoretical analysis, a series of honeycomb paperboards with different size dimension of paper honeycomb core had been set up in the FEA software. Then a packaging system which made up of rigid body and deformable body had been analyzed. The results show that the physical dimension of paper honeycomb core has a great effect on its impact resistance: with the increasing on degree of irregularity of paper honeycomb core, the peak acceleration has a quickly alteration. At the same time, when the length of glued edge is in near 4 mm and the girth of honeycomb core is 36mm, honeycomb paperboard can improve the energy absorption ability in the condition of elastic deformation. The research results can be used to optimize the structure design.