TThe multiphysics simulations for the microwave heating on the chemical reaction have been deemed as an efficient way to optimize the microwave treating process and avoid the safety problems coursed by the high power microwave energy applied. Unfortunately, most of the multiphysics simulations for the microwave heating on the chemical reaction only involve the Electromagnetics and Heat transfer modules and treat the physical properties as constant values; ignoring the influent of variation of the chemical reaction status. Compared to the previous model, Chemical Reaction Engineering and Mass Transfer have been added and a simplified bivariate characterization for effective permittivity was employed in the new model. Therefore, all properties are automatically updated by the reaction solution’s component and temperature. Meanwhile, the influence of the nature convection for heat and mass transfer is discussed. The problems such as manual update for the properties; complex characterization function for effective permittivity; thermal properties only updated by the chemical components; ignore the influence of nature convection for the temperature diffusion and less information about chemical reaction system in previous model can be avoided. The temperature diffusion coursed by nature convection has also been discussed. Integrative calculation for microwave process of biodiesel production is done in this study. Good agreement can been seen between the experimental and simulated results.