Abstract: A study on microwave assisted extraction (MAE) for berberine in Mahonia bealei was carried out in batch equipment. The mechanism of the extraction related to structural changes in the glands was discussed. The extracts were analyzed at 347nm by ultraviolet visible spectrophotometry. The parameters such as the solvent types, the intensity of microwave energy, the ratio (g/mL) of material to solvent volume were studied. The efficiency of microwave assisted extraction of different humidity material was investigated and optimized by means of the three factor and three level factorial design. Electron micrographs showed the mechanism of the extractions was related to structural change of the cells.