We investigate the relaxation dynamics of crystalline stems in relation to the molecular topology of the crystalline/amorphous interface, employing coarse-grained molecular dynamics. To efficiently generate model semicrystalline systems of linear polyethylene with a realistic interphase morphology, we simplified the Monte Carlo method by introducing molecular dynamics for faster relaxation. The structural properties of the generated systems are validated against experimental measurements, theoretical predictions, and existing simulation data. The models suggest that the probability distribution of loop-entry sites on the lamellar surface can be described by a power law in terms of the distance between the entry sites. By considering realistic interphase morphology, we are able to improve the prediction of the overall activation energy for the relaxation of crystalline stems, aligning it closely with experimental measurements. The largest model predicts that crystalline stems connected via large loops, i.e., those that exceed the entanglement length, and long tails are associated with increased activation energy; whereas stems connected to shorter tails show the lowest activation energy. These predictions can guide the future development of tougher semicrystalline polymers by providing insights into how amorphous chain morphology contributes to the activation energy and the relaxation dynamics of crystalline chains.