In this study, aiming at optimization of a novel continuous biodiesel production system was developed by com-bining technologies based on microwaves and magnetic fields. Factors affecting microwave-assisted biodiesel (alkyl esters) production reaction were analyzed in this investigation. Studied factors included magnetic field in-tensity (0, 0.225 and 0.450 T), microwave power (400, 821, and 1181 W), percentages of KOH and NaOH catalysts at constant concentrations of 1 wt％(0, 50％and 100％), and percentages of ethanol and methanol at a constant molar ratio of 6:1 (0, 50％and 100％). Response Surface Methodology (RSM) was used to optimize the reaction conditions. RSM-based analysis indicated that, all independent parameters had significant effects on the reaction efficiency. Results of the investigations reveal that the largest effects on the conversion efficiency were due to type of alcohol and magnetic field intensity. The optimized conditions were found to be a magnetic field intensity of 0.331 T, a microwave power of 677.77 W, catalyst percentages of 30.35％and 69.65％for KOH and NaOH, re-spectively, and alcohol percentages of 80.47％and 19.53％for methanol and ethanol, respectively. Under the op-timal conditions, yield of the reaction was 96.2％.