Poly(1-trimethylsilyl-1-propyne) (PTMSP), the most permeable polymer known, undergoes rapid physical aging. The permeability of PTMSP to gases and vapors decreases dramatically with physical aging. Cavity size (free volume) distributions were calculated in as-cast and aged PTMSP, using an energetic based cavity-sizing algorithm. The large cavities found in as-cast PTMSP disappear in aged PTMSP, which is consistent with the positron annihilation lifetime spectroscopy (PALS) measurements. We also characterized the connectivity of cavities in both as-cast and aged PTMSP membranes. Cavities are more connected in as-cast PTMSP than in aged PTMSP. The average cavity sizes calculated from computer simulation are in good agreement with PALS measurements. The transport and sorption properties of gases in as-cast and aged PTMSP are also measured by molecular simulation. Computer simulations showed the decrease of permeability and the increase of permeability selectivity in PTMSP membranes with physical aging, which agrees with experimental observations. The reduction in gas permeability with physical aging results mainly from the decrease of diffusion coefficients. Solubility coefficients show no significant changes with physical aging.