A traditional method of cooking fish known as fish boiling in which microwave irradiation was used instead of conventional external gas heating was investigated, and the microwave cooking process was studied and simulated via a three-dimensional finite element computational model. Although this cooking method is complex in that it contains both liquid and solid materials, and convection occurs inside the liquid during processing, the changes in temperature were successfully predicted by coupling the analysis of the electromagnetic field and heat transfer. We proposed an easier way to simulate the temperatures of the liquid inside which free convection occurred during heating. The appropriate value of the thermal conductivity of the liquid material for microwave cooking was validated by the experiment. On the basis of simulated temperature profiles and the parameters deduced from Differential Scanning Calorimetry (DSC) experimental data, the time-dependent degrees of protein denaturation during cooking were also estimated. The temperature and denaturation information were finally formatted in Femap and animated so that they could be investigated easily. (C) 2014 Elsevier Ltd. All rights reserved.