Molecular dynamics and mesoscale dynamics simulation techniques were used to investigate the effect of hydrogen bonding on the microphase separation, morphology and various physicochemical properties of segmented silicone-urea copolymers. Model silicone-urea copolymers investigated were based on the stoichiometric combinations of alpha,omega-aminopropyl terminated polydimethylsiloxane (PDMS) oligomers with number average molecular weights ranging from 700 to 15,000 g/mole and bis(4-isocyanatocyclohexyl)methane (HMDI). Urea hard segment contents of the copolymers, which were determined by the PDMS molecular weight, were in 1.7-34% by weight range. Since no chain extenders were used, urea hard segments in all copolymers were of uniform length. Simulation results clearly demonstrated the presence of very good microphase separation in all silicone-urea copolymers, even for the copolymer with 1.7% by weight hard segment content. Experimentally reported enhanced properties of these materials were shown to stem from strong hydrogen bond interactions which leads to the aggregation of urea hard segments and reinforcement of the PDMS.