Amorphous poly-para-xylylene (PPX) polymers were constructed using molecular mechanics (MM) and NVT+NPT-annealing methods. They provide the cut-off free volumes to absorb and transfer gas molecules. The corresponding sorption and diffusion properties were determined via Grand Canonical Monte Carlo (GCMC), NVT-Molecular Dynamics (MD) and cluster analysis methods. The results showed that temperature and pressure influence the sorption properties of gases obviously, but not to the diffusion coefficients of gases. Analyzing on the mean square displacement (MSD) data, this work finds that gases walk randomly through amorphous PPX polymers. The relative cluster permeability approaches to the experimental data.