The inclusion complexes between daidzein and three cyclodextrins (CDs), namely β-cyclodextrin (β-CD), methyl-β-cyclodextrin (Me-β-CD, DS = 12.5) and (2-hydroxy)propyl-β-cyclodextrin (HP-β-CD, DS = 4.2) were prepared. The effects of the inclusion behavior of daidzein with three kinds of cyclodextrins were investigated in both solution and solid state by methods of phase-solubility, XRD, DSC, SEM, ¹H-NMR and 2D ROESY methods. Furthermore, the antioxidant activities of daidzein and daidzein-CDs inclusion complexes were determined by the 1,1-diphenyl-2-picryl-hydrazyl (DPPH) method. The results showed that daidzein formed a 1:1 stoichiometric inclusion complex with β-CD, Me-β-CD and HP-β-CD. The results also showed that the solubility of daidzein was improved after encapsulating by CDs. ¹H-NMR and 2D ROESY analyses show that the B ring of daidzein was the part of the molecule that was most likely inserted into the cavity of CDs, thus forming an inclusion complex. Antioxidant activity studies showed that the antioxidant performance of the inclusion complexes was enhanced in comparison to the native daidzein. It could be a potentially promising way to develop a new formulation of daidzein for herbal medicine or healthcare products.