Abstract Daidzein (7,4′‐dihydroxyisoflavone) was phosphorylated by a modified Atherton‐Todd reaction. The structures of the five target product, were determined by X‐ray, IR, NMR and ESI‐MS. Electrospray ionization results show that in the gas phase all the phosphorylated daidzein derivatives could form non‐covalent complexes with the protein lysozyme, while non‐covalent complexes were not detected in the mixed solution of daidzein with lysozyme. Relative affinity of every non‐covalent complex was obtained according to its different decomposition orifice voltage.