As a new type of clean energy, biodiesel has been paid more and more attention. According to the existing methods of preparing biodiesel by chemical method, there are many disadvantages such as long reaction time, high energy consumption and serious environmental pollution. A new type of continuous flow microwave reactor is designed for the preparation of biodiesel. The electromagnetic field, chemical reaction kinetics, laminar flow and heat and mass transfer are coupled with multiple physical fields to simulate the reaction process through Coｍsol Multiphysics. By analyzing the effect of reactant flow rate on temperature, and by analyzing the effect of coil turns, coil spiral size and cavity size on the energy utilization ratio, the overall reactor structure size is optimized to improve the energy utilization ratio and increase the handling capacity of the reaction materials.