<p>A coarse-grained polymer model based on the modified finite-extensible nonlinear elastic (FENE) bond potential and the Lennard–Jones interaction—originally inspired by the widely used Kremer–Grest framework—has recently been shown to spontaneously form semicrystalline structures containing hexagonally packed crystalline domains. These findings suggest that such minimal bead–spring models can serve as fundamental representations of polymer lamellae. However, the intrinsic periodicity of lamellae inevitably interacts with the finite simulation box under periodic boundary conditions, making it challenging to construct reliable semicrystalline morphologies. In this study, we generated well-defined lamellar structures using this crystallizable FENE–LJ model and systematically investigated how the simulation box size influences lamellar spacing and crystallinity. We found that when the lateral dimensions of the simulation box were not sufficiently large, artifacts emerged, including delayed relaxation of crystallinity and abnormal tilt angles within the crystalline layers. These distortions indicate that inadequate box dimensions can compromise the intrinsic molecular organization of lamellae. By systematically varying the box size, we identified the minimum periodic simulation domain required to obtain physically reasonable lamellar morphologies in this crystallizable FENE–LJ polymer model. Our findings provide practical guidelines for constructing semicrystalline structures in molecular simulations and contribute to a deeper understanding of finite-size effects in polymer crystallization.</p>