According to the standard of GB/T1500.3-2008 and the guidelines of ISO/REMCO, the preparation of National Certified Reference Materials (CRMs) of active compounds was composed of the following two aspects: preparation and certification. This paper presents an example of the preparation of biochanin A to illustrate the preparation of National CRMs of active compounds from natural products. Firstly, the target compound was extracted and purified from crude materials. Then,its chemical structure was identified by UV spectrum, IR spectrum, ESI-MS, and NMR. The purity of the compound was determined by HPLC with the area normalization method. The certified value assessed by comparing the purity values from six independent qualified laboratories and the value of uncertainty were given. Thermal analysis, residual solvent, homogeneity testing and stability testing was tested in the process.