The microwave assisted thermal sterilization computer simulation model (MATS-CSM) was developed to improve the previous computer simulation model for the microwave assisted thermal sterilization (MATS) system. Development of the new MATS-CSM included determination of optimum heating time step, evaluation of electromagnetic field distribution and the resulting heating pattern in food, and experimental validation of heating patterns. It was determined that the minimum number of discretization that would not cause immediate divergence of the EM-heat transfer solution was 32 steps corresponding to 97 mm and 5.6 s of displacement and heating time for every step, respectively. Furthermore, this study successfully demonstrated the symmetrical electromagnetic field distribution between top and bottom microwave entry ports and a staggered electric field pattern from one cavity of the MATS to the next. In addition, MATS-CSM confirmed that incorporating heat diffusion in the simulation model reduces the difference in hot spot and cold spot temperature by 65%. It also confirmed that water circulation reduces the edge heating effect, as observed in experiments. The heating pattern generated by MATS-CSM was verified experimentally through a chemical marker method. Based on the percent areal cross section of the weighted average temperature, there were no noticeable differences between the heating zones generated by the MATS-CSM and by the chemical marker method. The percent areal cross section of the cold area 1, cold area 2, and hot area by MATS-CSM were 35%, 25%, and 40%, respectively, and the cold area 1, cold area 2, and hot area by chemical marker method were 35%, 30%, and 35%, respectively. (C) 2013 Elsevier Ltd. All rights reserved.