Deep body temperature reveals individual physiological states, and is important in patient monitoring and chronobiological studies. An innovative dual-heat-flux method has been shown experimentally to be competitive with the conventional zero-heat-flow method in its performance, in terms of measurement accuracy and step response to changes in the deep temperature. We have utilized a finite element method to model and simulate the dynamic process of a dual-heat-flux probe in deep body temperature measurements to validate the fundamental principles of the dual-heat-flux method theoretically, and to acquire a detailed quantitative description of the thermal profile of the dual-heat-flux probe. The simulation results show that the estimated deep body temperature is influenced by the ambient temperature (linearly, at a maximum rate of 0.03 °C/°C) and the blood perfusion rate. The corresponding depth of the estimated temperature in the skin and subcutaneous tissue layer is consistent when using the dual-heat-flux probe. Insights in improving the performance of the dual-heat-flux method were discussed for further studies of dual-heat-flux probes, taking into account structural and geometric considerations.