A novel method is presented to build semicrystalline polymer models used in molecular dynamics simulations. The method allows controlling certain aspects of the molecular morphology of the material. It relies on the generation of the polymer sections in the amorphous phase of the semicrystalline structure according to the statistical polymer physics theory proposed by Adhikari and Muthukumar ( J. Chem. Phys.2019, 151, 114905). The amorphous phase is first built based on the method initially developed by Theodorou and Suter ( Macromolecules1985,18 (7), 1467-1478). Then, the amorphous phase is stacked between crystallites, and a connection algorithm proposed by Rigby et al. ( Advanced Composites for Aerospace, Marine, and Land Applications; Springer: Cham, Switzerland, 2014), initially developed to build polymer thermosets, is employed to link the two phases. For a given set of degree of crystallinity, semicrystalline long period, densities of the crystalline and amorphous phases, and polymer molecular weight, the characteristic ratio is used to control the relative fractions of different types of polymer sections in the amorphous phase as well as the distribution of their lengths. There are three types of amorphous polymer sections: the ones that are reentering in the same crystallite called loops, those that are bonding two different crystallites called tie chains, and the chain tails ending in the amorphous region. The higher the imposed characteristic ratio is, the higher the fraction of the tie chains is. The full implementation of the theory is described and then applied to high-density polyethylene (HDPE). Several samples are generated. The obtained structures are characterized. Their elastic coefficients are computed, and high uniaxial deformations are performed. It is shown that the higher the degree of crystallinity, the higher the elastic coefficients. An entanglement analysis shows that the quantity of tie chains is more decisive than the entanglements in acting as stress transmitters to rigidify the structure.