The aim of this work was firstly to do a precise thermal analysis of microwave assisted production of biodiesel. In this paper, the effective permittivity of biodiesel synthesis was updated with two methods: a traditional method and a bivariate function of temperature and concentration of one component, then the thermal analysis of the reaction process were accomplished with multi-physics calculation. The results show that there exists large distinction in temperature between these two simulation results calculated by the two methods. The two hot spots locate in the opposite side and their temperature's difference is up to 9 degrees C when the reaction is just carried out for 18 s. But the temperature risings and distributions calculated by the new method are closer to the measured results. The thermal analysis based on the new method will be helpful for the industrial design of biodiesel production. Crown Copyright (C) 2013 Published by Elsevier Ltd. All rights reserved.