The anionic polyurethane nanoparticles (APU-NPs) were obtained by an emulsion polymerization method. It was found that the average size of the prepared APU-NPs is about 84 nm, and the APU-NPs have zeta-potential of -38.9 mV. The bulk characterization of synthesized APU-NPs was investigated by FTIR. The blood compatibility of APU-NPs was characterized by in vitro for coagulation tests, complement activation, platelet activation, cytotoxicity experiments, and hemolysis assay. The results showed that the APU-NPs synthesized in this paper are blood compatible with low level of cell cytotoxicity, and the results were significant for their potential use in vivo.