Abstract In order to provide a quantitative disclosure on the RFA (radiofrequency ablation)-induced thermal ablation effects within thyroid tissues, this paper has developed a three-dimensional finite element simulation strategy based on a MRI (magnetic resonance imaging)-reconstructed model. The thermal lesion's growth was predicted and interpreted under two treatment conditions, i.e. single-cooled-electrode modality and two-cooled-electrode system. The results show that the thermal lesion's growth is significantly affected by two factors including the position of RF electrode and thermal–physiological behavior of the breathing airflow. Additional parametric studies revealed several valuable phenomena, e.g. with the electrode's movement, thermal injury with varying severity would happen to the trachea wall. Besides, the changes in airflow mass produced evident effects on the total heat flux of thyroid surface, while the changes in breathing frequency only generated minor effects that can be ignored. The present study provided a better understanding on the thermal lesions of RFA within thyroid domain, which will help guide future treatment of the thyroid cancer.