The molecular-weight-controlled poly(amic acid) (PAA) resin functionalized with phenylethynyl end-groups were prepared via the polycondensation of 3,3′,4,4′-biphenyltetra-carboxylic dianhydride (BPDA), 4,4′-oxydianiline (ODA) and 4-phenylethynyl phthalic anhydride (PEPA) served as molecular-weight-controlling and reactive end-capping agent. The PAA resin with relatively high concentration were employed to form the PAA film by solution-cast method, which was then thermally converted to the fully-cured polyimide (PI) film. The aggregation state of the PI film with flexible main-chain structure and relatively high molecular weights was investigated systematically by XRD and dynamic thermo-mechanical analysis. It is found that the degree of polymer chain order caused by thermal imidization counteracts that of chain segment disorientation induced by elevated temperature. The covalent incorporation of chain-extension structures in the backbones, induced by thermal curing of phenylethynyl groups, might slightly constrain the configuration of ether and biphenyl linkages, and facilitate ordered in-plane oriented micro-regions, thereby strengthening and toughening the PI film.