The purity characterization method for genistein certified reference material was established, and the its uncertainty generated during characterization was evaluated. In this study, we qualitatively analyzed genistein samples by Fourier transform infrared spectroscopy, mass spectrometry, and nuclear magnetic hydrogen spectrometry. Thereafter, two independent methods were used in the purity measurement of certified reference material (CRM) of main components. Moreover, the uniformity, stability and the uncertainty introduced in the whole setting were evaluated. Finally, the purity of the genistein CRM was confirmed to be 99.6%, and the expanded uncertainty was 0.4% (k=2).