Flavonoids are the most widely used in the field of the food, medicine, and cosmetic due to their pharmacological functions and biological activities, such as anti-tumor, anti-inflammatory and antioxidation. This work described the assignment of purity values to 3 flavonoids certified reference materials (CRMs) including baicalein, 5,7-dihydoxy flavones and naringenine which were developed in this study according to the ISO Guides 34 and 35. The qualitative analysis was performed by liquid chromatography-mass spectrometry (LC-MS) and infrared spectroscopy (IR). The CRMs’ purity values were assigned based on the weighted average of quantitative nuclear magnetic resonance method and mass balance approach with high resolution liquid chromatography-VWD. All the three CRMs with following value mass fractions: baicalein at a certified purity P ± U (k = 2) of 98.8% ± 0.8%; 5,7-dihydoxy flavones of 99.1% ± 0.7% and naringenine of 99.5% ± 1.0% respectively. The homogeneity of the CRMs was determined by an in-house validated liquid chromatographic method. Potential degradation during storage was also investigated and a shelf-life based on this value was established.