Cyclodextrins (CDs) can improve the solubility and stability of flavonoids by forming supramolecular complexes. However, the detailed inclusion mechanism has not been fully elucidated. In this study, the binding ability of eight flavonoids with four common CDs (α-, β-, methyl-β-, γ-CD) was investigated. Then, the interaction characteristics of two flavonoids (Dihydromyricetin (DMY) and Naringenin) with M-β-CD were further explored by using phase solubility, ultraviolet, infrared, X-ray diffraction, differential scanning calorimetry, molecular docking and ONIOM calculations. The results indicated that the molecular volume of flavonoids and the cavity size of CDs have distinct effects on the host-guest interaction. DMY and Naringenin form stable supramolecular complexes with M-β-CD mainly through hydrophobic interactions and Van der Waals forces. In addition, the stability of the Naringenin/m-β-CD is higher than that of DMY/M-β-CD, which is consistent with the experimental stability constant. Both of the above flavonoids entered the large hole of the hydrophobic cavity of M-β-CD through one end of the B-ring, which has a significant contribution to the formation of the host-guest hydrogen bonds. Taken together, this study is helpful to further understand the interaction mechanism between CDs and guest molecules, expand the application of CDs, and promote the utilization of natural active compounds.