Thermal Pasteurization of Eggs, as a widely used nutritive food, has been simulated. A three‐dimensional numerical model, computational fluid dynamics codes of heat transfer equations using heat natural convection, and conduction mechanisms, based on finite element method, was developed to study the effect of air cell size and eggshell thickness. The model, confirmed by comparing experimental and numerical results, was able to predict the temperature profiles, the slowest heating zone, and the required heating time during pasteurization of intact eggs. The results showed that the air cell acted as a heat insulator. Increasing the air cell volume resulted in decreasing of the heat transfer rate, and the increasing the required time of pasteurization (up to 14%). The findings show that the effect on thermal pasteurization of the eggshell thickness was not considerable in comparison to the air cell volume.