Molecular dynamics simulations using fully atomistic models were conducted to investigate gas transport mechanism and its connection to the free volume distribution and morphology in polyvinyl chloride (PVC) and in PVC modified with 4-fluorothiophenol. The influence of both, modification degree and temperature on diffusion mechanism was thoroughly studied. The diffusion coefficients of O-2 and N-2, were determined via molecular dynamics simulation using the COMPASS forcefield over a range of temperatures (375, 400, 425, and 450 K) using up to 200 ns simulation time. The introduction of pendant bulky groups along the polymer backbone results in a less ordered polymer matrix increasing the free volume available and consequently the diffusion coefficients of both gases, O-2 and N-2. Additionally, the temperature range selected in this work allows us to investigate the crossover from a solid-like diffusion mechanism (at low temperatures) to a liquid-like mechanism that takes place at higher temperatures. The gas transport coefficients of these polymers obtained from MD simulations were compared with previously reported values in literature based on both experimental and simulation studies, and the results obtained were within the expectations indicating the viability of the approach.