In protein adsorption on material surfaces, the surface structure at the nanometer-scale is one of the most important factors; however, the relationship between the size of the hydrophobic protein-adsorptive domain and that of the protein in protein adsorption remains unclear. In this study, we prepared phase-separated surfaces with different hydrophobic domain sizes (10 or 20 nm) using amphiphilic ABA-type block copolymers composed of hydrophilic poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC) and hydrophobic poly(3-methacryloyloxy propyltris(trimethylsilyloxy) silane) (PMPTSSi) to investigate the adsorption behavior of proteins, including fibronectin, fibrinogen, and lysozyme. The hydrophobic PMPTSSi domain promotes protein adsorption, whereas the PMPC domain suppresses this. Compared with the uniform hydrophobic PMPTSSi surface, fibronectin and fibrinogen were not adsorb on the phase-separated surfaces, while lysozymes adsorbed only partly, indicating that proteins smaller than nanoscale hydrophobic domains adsorbed on the phase-separated surface. Moreover, the protein adsorption behavior and circular dichroism spectra analysis suggest that lysozyme densely adsorbed on the hydrophobic domain like a multi-layer, and that denature on the surface was promoted. This study contributes to the understanding of protein adsorption at nanoscale interfaces and designing biomaterials.