In this study, we report on the effect of thermal treatment on polyimide precursors (HPIs) and on the resulting thermally rearranged polybenzoxazole (TR-PBO) polymer membranes as investigated through the use of molecular dynamics (MD) simulations. For this purpose, we have first analyzed the structures of hydroxy-containing polyimides before thermal treatment and those of the thermally rearranged polybenzoxazoles after the thermal treatment, according to their temperature conditions. As expected, HPIs and TR-PBOs always show very limited motion of their polymer chains, indicated by the radius of gyration, due to their well-known thermal stability. In particular, the very rigid and stiff PBO linkages did not undergo significant change in their torsional angle distribution. On the other hand, in regards to intrachain movement, HPI chains were significantly affected by temperature. Their conformational changes were notably observed, which affected the distances between possible reaction sites, oxygen atoms in hydroxyl groups, and carbon atoms in the imido-ring. The free volume analysis, performed on both polymers and during thermal treatment, indicates that HPIs have a unimodal distribution of free volume areas, which partially coalesce in larger areas having, however, a relatively narrow size. Further, TR-PBO shows a bimodal cavity distribution, and after thermal treatment and TR reaction, the free volume structures in TR-PBO are maintained. The cavity size distributions determined by simulation were also consistent with free volume distributions determined by positron annihilation lifetime spectroscopy.