Abstract: The purpose of this study was to explore the interaction mechanism between glycyrrhiza protein and berberine in the decocting process of Rhizoma Coptidis and Liquorice and its effect on the pharmacodynamic effect. In this experiment, licorice crude protein was obtained from licorice decoction pieces, and it was found that licorice crude protein and berberine could form spherical supramolecular particles after decocting together. Morphological characterization was carried out by using Malvin particle size analyzer and emission scanning electron microscopy, and the supramolecular particles were observed to be nanoscale, which was significantly different from the morphology of licorice protein and berberine. The results of ultraviolet, infrared and fluorescence spectroscopy showed that the mechanism of molecular interaction was induced by weak bonds such as electrostatic attraction and hydrophobic interaction. Furthermore, the antimicrobial activity of berberine was significantly affected by the supramolecular particles of licorice protein-berberine, which were significantly different from the mechanical mixture. This study reveals the pharmacological value of macromolecular substances such as proteins in the decoction of licorice and Coptis chinensis from a new perspective, which is helpful to promote the secondary development of clinical effective prescriptions, especially the research on the pharmacological substance basis of classic famous prescriptions.