Abstract The inclusion behavior, inclusion capacity and inclusion mode of pinocembrin (PIN) with dimethyl-β-cyclodextrin (DM-β-CD) and trimethyl-β-cyclodextrin (TM-β-CD) were characterized by X-ray diffraction (XRD), thermal analysis, scanning electron microscopy (SEM), UV-visible spectral titration and molecular docking. The results showed that the packing ratio of PIN/DM-β-CD complex and PIN/TM-β-CD complex was 1:1. The water solubility of PIN increased by 817 times and 575 times in the inclusion complex with DM-β-CD and TM-β-CD, respectively. Molecular docking showed the PIN entered from the large end of the DM-β-CD molecule and penetrated through the cavity. The A and B rings of the PIN were respectively located at the big and small ends of the CD molecule. For the TM-β-CD, only A and C rings of the PIN entered the cavity of CD.