Coarse-grained molecular dynamics simulations can model the deformation and fracture processes of the lamellar structure in polyethylene on a molecular scale; however, the simulations have not been performed due to the difficulty in building the structure and the limitations of small-scale simulations on the order of 104 beads. Thus, we propose a crystallization method for a large-scale lamellar structure on the order of 106 beads. The highly oriented lamellar structure is stretched in a coarse-grained molecular dynamics simulation. The stress and variation of crystallinity during stretching parallel and perpendicular to the crystal direction agree with experimental results, confirming the validity of our simulation results. During stretching parallel to the crystal direction, the amorphous layers crystallize and the crystalline layers fragment. We also find that the movement of the polymer chain ends from amorphous to crystalline layers, which is difficult to observe experimentally, increases the compression and generation of voids in the amorphous layers.