AbstractGenistein (Gen) has great potential in the field of anti‐tumor, however, its low solubility in water, serious biotoxicity on thyroid function and estrogenic effects limit its further clinical application. Host‐guest inclusion complex based on supramolecular chemistry could be a promising strategy to address these issues. During last decades, cyclodextrin as one of the most popular supramolecular hosts have been considered as a promising drug delivery carrier. Herein, the host‐guest encapsulation system of Gen with amino‐appended β‐cyclodextrins (ACDs) were reported, and inclusion complexes have been characterized by 1H and 2D‐ROESY nuclear magnetic resonance (NMR), Phase solubility curve, Fourier transform infrared spectroscopy (FT‐IR), X‐ray powder diffraction (XRD) and scanning electron microscopy (SEM). The results showed that Gen was successfully encapsulated into the cavities of ACDs to form the complexes with 1 : 1 stoichiometry, and compared with free Gen, the aqueous solubility of the complexes was enhanced by 1000 folds. In addition, the cytotoxicity of their complexes to tumor cell line HEK293T was significantly improved. These results will be potentially useful for the development of further clinical application of genistein‐based anticancer agent.