Pre-imidization has been found to have a determining role on the final properties of polyimide (PI) films. In this work, a series of 4,4'-(hexafluoroisopropylidene)diphthalic anhydride (6FDA)/2,2'-bis(trifluoromethyl)benzidine (TFMB) PI models with specified pre-imidization degree (pre-ID) were constructed and analyzed on the basis of molecular dynamic (MD) simulation to reveal the real-time evolution of structure and properties that occurred during the pre-imidization process. The MD results indicated that the Tg of the models increased obviously with increasing pre-ID, which corresponded to the increase of rigid PI chain segments that restricted the mobility of molecular chains. In addition, the increase of fractional free volume and mean square end-to-end distance indicated looser chain packing and more extended chain conformation during the pre-imidization process. As a further verification, a series of corresponding PI films were experimentally prepared via a controlled partially pre-imidization process. Mechanical properties of the prepared PI films were tested to be significantly enhanced, and the coefficient of thermal expansion decreased from 61.5 to 47.6 ppm/°C with pre-ID increasing from 0% to 100%, which could be attributed to the orderly molecular chain arrangement formed during the chemical pre-imidization process, as disclosed by MD simulation. This work paves the way for the observation of the real-time structure and property evolutions of PI materials, especially during the pre-imidization process.