Polyhedral Oligomeric Silsesquioxane (POSS)–polyimide (PI) thin films were synthesized from pre-mixed solution of oxydianiline–pyromellitic dianhydryde (ODA–PMDA) and TriSilanolPhenyl (TSP) POSS. POSS–PI polymerization reaction kinetics was studied using Fourier Transform Infrared (FTIR) spectroscopy. The POSS–PI films were then investigated by tensile tests, followed by surface morphology examination using Atomic Force Microscopy (AFM) and Environmental Scanning Electron Microscopy (ESEM). An interdisciplinary approach was applied for establishing a relation between POSS–PI composites chemical microstructure properties and failure mechanisms. Inter molecular POSS–POSS interaction by either phase separation, or chemical POSS–POSS condensation reaction were observed as key factors, affecting the nanocomposite mechanical properties via formation of aggregates. The amount and density of these aggregates were shown to be composition dependent. A model based on formation and coalescence of voids during tensile tests was suggested for understanding the effect of the POSS content on the POSS–PI mechanical response.