Polyurethanes (PU) and their polymeric derivatives are widely used in the manufacturing of medical devices. It is important to understand how protein adsorbs onto PU materials as this molecular process directly implicates surface biocompatibility. In this work, we compared protein adsorption at the PU film surfaces with that from the hydrophilic silicon oxide. Two PU polymers were used, a commercial polyurethane (PUA) and a novel poly(carbonate-urea)urethane matrix containing silsesquioxanes (PU4). AFM imaging revealed micro-domain segregation on both PU surfaces, but the incorporation of pendent silsesquioxanes made the PU4 surface much rougher, with the outer surface comprised of soft upper PU segments and lower PU-silsesquioxane hard segments. It appeared that fibrinogen was preferable to adsorb onto the upper soft PU segments. The spectroscopic ellipsometry (SE) measurements at the PU film/solution interface showed that human serum albumin (HSA) adsorption was little affected by surface chemistry whilst fibrinogen adsorption was much greater on the two PU surfaces indicating a strong surface effect. Further studies revealed that HSA adsorption was reversible on hydrophilic SiO2 against changes in pH from 5 to 7, but irreversible on the two PU surfaces. In contrast, fibrinogen adsorption against the same pH cycling was found to be irreversible on all three surfaces. The different extent of irreversibility was clearly indicative of different interfacial interactions. Sequential protein adsorption revealed that the PU4 surface shared similar physiochemical properties to the SiO2 surface, demonstrating the success in incorporating the siloxane pendant nanocages. The knowledge of protein surface structure and behaviour may lead to the development of effective means to control surface biocompatibility.