This research aimed to provide an understanding of the selection and safe application of pipeline liner materials for hydrogen transport by examining the permeation properties and mechanisms of hydrogen within polymers commonly used for this purpose, such as high-density polyethylene (HDPE) and ethylene-vinyl alcohol copolymer (EVOH), through molecular simulation. The study was carried out within defined operational parameters of temperature (ranging from room temperature to 80 °C) and pressure (from 2.5 to 10 MPa) that are pertinent to hydrogen pipeline infrastructures. The results reveal that with an increase in temperature from 30 °C to 80 °C, the solubility, diffusion, and permeability coefficients of hydrogen in HDPE increase by 18.7%, 92.9%, and 129.0%, respectively. Similarly, in EVOH, these coefficients experience increments of 15.9%, 81.6%, and 112.7%. Conversely, pressure variations have a negligible effect on permeability in both polymers. HDPE exhibits significantly higher hydrogen permeability compared to EVOH. The unique chain segment configuration of EVOH leads to the formation of robust hydrogen bonds among the hydroxyl groups, thereby impeding the permeation of hydrogen. The process by which hydrogen is adsorbed in polymers involves aggregation at low potential energy levels. During diffusion, the hydrogen molecule primarily vibrates within a limited range, with intermittent occurrences of significant hole-to-hole transitions over larger distances. Hydrogen exhibits a stronger interaction with HDPE compared to EVOH, leading to a higher number of adsorption sites and increased hydrogen adsorption capacity in HDPE. Hydrogen molecules move more actively in HDPE than in EVOH, exhibiting greater hole amplitude and more holes in transition during the diffusion process.