Microwave-assisted extraction (MAE) technique was employed and optimized for microwave power, irradiation time and solvent (ethanol) concentration using a central composite design and response surface methodology for the efficient extraction of bioactive alkaloid compounds from Rhizoma coptidis (Coptis chinensis Franch.). Alkaloid compounds were successfully isolated and quantified by high-performance liquid chromatography with ultraviolet detection. Maximum yields of alkaloid constitutes were predicted based on desirability option, and optimal conditions for MAE were microwave power of 180W, irradiation time of 5min, and ethanol concentration of 50%. Reliability of the method was confirmed by verification experiments performed under optimal conditions, and the experimental values (TAC of 333.94 mg BCE/g d.w., BC of 71.43 mg BCE/g d.w., and PC of 15.58 mg PCE/g d.w.) matched well with estimated values, suggesting that the estimated models were reliable and valid for MAE of alkaloids.