The quantity and secondary structure of adsorbed albumin (Alb) and immunoglobulin G (IgG) on two kinds of biomaterial surfaces-polyurethane (PU (H50-50)) and polystyrene (PS) were studied using Fourier transform infrared spectroscopy (FTIR). The original spectra tested by FTIR were processed using second-derivation and self-deconvolution techniques to obtain the content of different secondary structures of adsorbed proteins, which could be used to evaluate the denatured degree of proteins. Results showed that the quantity of Alb adsorbed on PU (H50-50) surface is larger than PS. The hydrophobic features of material played a role in conformational change of adsorbed protein, and indicated that the denatured degree caused by hydrophobic PS was greater than hydrophilic PU (H50-50). The blood compatibility of PU (H50-50) was likely to be better than PS.