The aim of this paper is to study the mechanical properties of the honeycomb paperboard core layer with the re-entrant hexagonal honeycomb structure, and to provide a theoretical basis for the transportation and packaging design of the paperboard with re-entrant hexagonal honeycomb core (PRHHC). Finite Element Method (FEM) is used to analyze the in-plane load-bearing performance of the PRHHC under the influence of different structural parameters. After research, it is found that when the length of the horizontal cell wall of the PRHHC decreases, other structural parameters remain unchanged, the plateau stress in the in-plane direction increases. The standardized stress in the plateau stage of energy absorption increases, and its best energy absorption point also rises. The size of the structural parameters of the PRHHC has a huge impact on its plateau stress and energy absorption characteristics. Therefore, these investigations are of great significance to the development of honeycomb carton.