Berberine hydrochloride (BBH) is an isoquinoline alkaloid, and its diverse bioactivities have been studied for decades. However, BBH exhibits poor solubility and low oral bioavailability, which hampers its potential therapeutic exploitation. In this study, hydrosoluble Lysine‐modified β‐cyclodextrin (Lys‐β‐CD) was synthesized. Then BBH‐Lysine‐β‐cyclodextrin inclusion complexes (BBH/Lys‐β‐CD IC) were prepared by the co‐deposition method and optimized using the Box‐Behnken design. In addition, phase solubility was studied and showed that BBH and Lys‐β‐CD can form inclusion complexes in a stoichiometric ratio of 1 : 1. The morphological characterizations exhibited that the IC had an irregular sheet and layered structure. The results of FTIR and 1H NMR revealed that BBH entered the Lys‐β‐CD cavity with non‐covalent interactions between host‐guest molecules. Furthermore, the binding pattern of BBH with the Lys‐β‐CD was investigated by molecular docking study. The release behavior of IC showed that BBH could be released slowly from the inclusion complex. Hence, the Lys‐β‐CD IC has broad application prospects in drug delivery and biomedical fields.