We report that the nanometer-scale architecture of polymer chains plays a crucial role in its protein resistant property over surface chemistry. Protein-repellent (noncharged), few nanometer thick polymer layers were designed with homopolymer chains physisorbed on solids. We evaluated the antifouling property of the hydrophilic or hydrophobic adsorbed homopolymer chains against bovine serum albumin in water. Molecular dynamics simulations along with sum frequency generation spectroscopy data revealed the self-organized nanoarchitecture of the adsorbed chains composed of inner nematic-like ordered segments and outer brush-like segments across homopolymer systems with different interactions among a polymer, substrate, and interfacial water. We propose that this structure acts as a dual barrier against protein adsorption.