This comprehensive study explored the aging process of PIM-1, a ladder polymer of intrinsic microporosity (PIM), by applying molecular dynamics simulations for the first time. Through detailed analysis, our work illustrates the evolution of the polymer structure from a loosely packed, less dense state of the pristine polymer to a more tightly packed configuration due to physical aging. For this purpose, a novel molecular dynamics (MD) methodology was employed in the process toward equilibration of PIM-1. This structural transition was quantitatively captured by measuring key parameters such as density, fractional free volume (FFV), cohesive energy density (CED), d-spacing, surface area, and gas permeabilities. The simulations demonstrate a noticeable increase in density by approximately 7 % in aged PIM-1 compared to a fresh sample. This increase in density is accompanied by a corresponding decrease in FFV, suggesting a more compact molecular arrangement. The impact of these structural changes is evident in the gas transport properties. Permeabilities of all gases tested, He, H2, O2, N2, CO2 and CH4, decreased by 33 %–80 %. Moreover, the selectivity of gas pairs like CO2/CH4 and O2/N2 exhibited increasing trends due to aging, as previously reported in experimental work. Structural analysis performed on the fresh and aged structures indicated collapse of free volume over aging, by disappearance of pores larger than ∼6.5 Å. Furthermore, no intrachain rearrangement was observed during physical aging in the ladder PIM-1 structure; rather, the aging resulted in increased interchain packing efficiency. Our methodology can be employed to other PIM architectures, such as polyimides of intrinsic microporosity (PIM-PIs) as well as low-free volume glassy polymers.