Compared with Type III hydrogen storage vessels, the great advantages of Type IV hydrogen storage vessels are their large hydrogen storage density, less weight, and not prone to fatigue failure, which extends the service life. However, due to the penetration of hydrogen, buckling of the plastic liner will happen. Therefore hydrogen permeation behavior in the liner polymer materials of Type Ⅳ hydrogen storage vessels is an important problem. In order to investigate the hydrogen permeation in the liner material of type Ⅳ hydrogen storage vessels, the polyethylene and polyamide models were constructed by the Materials Studio (MS) molecular simulation software to simulate the diffusion and adsorption process of hydrogen molecules in polyethylene and polyamide under the temperature of 263–353 K. The influence of solubility coefficient, diffusion coefficient, and Fractional Free Volume on the permeability of gas molecules were also analyzed. The permeation mechanism of hydrogen in polyethylene and polyamide materials was investigated at molecular scale. The results show under the same conditions, solubility coefficient, diffusion coefficient and permeability coefficient of hydrogen in polyethylene are greater than those in polyamide. Under the simulated conditions in the paper, compared with polyethylene, polyamide shows better hydrogen permeability resistance.