Hybrid hyper-cross-linked membranes based on inorganic polyhedral oligomeric silsesquioxanes (POSS) covalently bonded with organic imides have been shown to maintain remarkable molecular sieving abilities and gas separation performances up to 300 C. These films are obtained through the interfacial polycondensation of POSS with a dianhydride, leading to a polyPOSS-(amic acid) network, which is then converted to a polyPOSS-imide network by thermal imidization. Using the pyromellitic (PMDA) dianhydride as a test case, the underlying molecular structures have been generated by molecular dynamics (MD) simulations and specific algorithms which closely mimicked the mixing, polycondensation and imidization steps of the experimental scheme. This allowed realistic models of the final cross-linked imide networks to be compared with their un-cross-linked monomer mixtures and their intermediate amic-acid precursors. Both the formation of the network and the subsequent imidization decreased the density as the systems became sterically more constrained. The volume shrinkage during imidization was less than expected considering the amount of water removal. This led to a larger void space and an improved gas solubility for the polyPOSS-imide films. Although the networks were constructed with the experimentally-found average of four linked arms per POSS, the distribution of the number of links per POSS were quite wide with a range from zero to the maximum possible of eight links per POSS. There was also considerable heterogeneity in the POSS imide POSS angles, which was related to the flexible aliphatic linker between the organic and inorganic moieties. Thermomechanical analyses confirmed that these cross-linked materials were well-suited for high-temperature applications. When subjected to uniaxial tension, they strain hardened at large deformations and their elastic moduli remained solid-like at high temperatures.