Abstract The molecular structure and chain packing morphology are shown to be the fundamental factors in determining the thermal-mechanical properties of polymer thin films. This is demonstrated for two polyimides, PMDA-ODA and BPDA-PDA, which have contrasting molecular structures with semi-flexible and rigid rod-like chain morphologies. We first examine the effect of molecular structure on the chain morphologies, then the influence of chain morphology on the materials properties. By examining the degree of anisotropy in materials properties between the lateral and vertical directions with respect to the film plane, a clear correlation between molecular structure and properties is observed. This is further manifested in the fracture behavior of metal-polyimide fine line structures, where the fracture characteristics are found to be largely controlled by the mechanical properties of the polyimide. A strong polyimide, BPDA-PDA, is found to have a fracture toughness about threefold higher than a soft polyimide, PMDA-ODA.