In the present study, the effects of loading, topology, and extraframework ions on SO2 diffusion in zeolites 13X and SA were investigated using molecular dynamics simulation. The study was performed at different loadings, that is, 4, 8, 16, and 32 molecules per unit cell (UC) and various temperatures, that is, 300, 400, 500, and 600 K. The simulation results showed that in the same SO2 loading and temperature, the self-diffusion coefficients in zeolite 13X are higher than those of SA, which can be attributed to the smaller pore window size along with strong electrostatic forces of Ca cations in SA. This result is in accordance with higher mean square displacements (MSDs) of SO2 molecules in zeolite 13X, in which more hopping can be observed between cages. A closer inspection of the MSD plots in a short time interval (e.g., 200 ps) demonstrates a stepwise behavior which is an important aspect of topology effects, where the hopping between cages and relaxation within cages take place. In both types of zeolites, the self-diffusion coefficient of SO2 molecules initially displays a slight increase at low loading and follows a slow decrease at high loading of SO2. Such a loading-dependent behavior can be attributed to various interactions between SO2-SO2 and SO2-zeolites/cations. With increasing the loading from 4 to 16 molecules/UC, although the SO2-SO2 interaction increases, interaction between SO2 molecules and zeolites (or cations) decreases, which leads to less restriction on diffusing SO2 molecules. However, increasing the loading from 16 to 32 molecules/UC eventually increases the collision frequency among gas molecules, which is unfavorable to the diffusion process, and therefore, self-diffusion decreases.