The aim of this communication is firstly to describe the effective permittivity of the biodiesel reaction for multiphysics calculation of microwave heating. An innovatively method was proposed to get the effective permittivity of the biodiesel reaction solution through one measurement, which can be directly applied for the thermal analysis of microwave heating on biodiesel reaction based on the multiphysics calculation. The effective permittivity of biodiesel reaction at any temperature and concentration obtained in this paper. The maximum relative error of real part is 4.10%, and 5.65% for imaginary part. The calculated results also show good agreement with the measured results at constant temperature. Crown Copyright (C) 2013 Published by Elsevier Ltd. All rights reserved.