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Thermal biological effect caused by millimeter waves is very complicated, there are many related parameters, including: the Incident Power Density (IPD), the frequency of millimeter waves, the exposure time, boundary conditions, blood flow, metabolic rates and so on. We built up a transient thermal multilayer model for heating of human skin by high power millimeter waves by finite volume method (FVM) based on Pennes' bioheat transfer equation in this paper. We analyzed the calculated results and compared them with the experimental ones. The errors were no more than 1 °C, especially at the incident power densities of 284 and 853 mW/cm2, the computing results agreed closely with the experimental ones. We analyzed the temperature at different depth of the skin, corresponding to different incident power densities, and the temperature changes in the energy penetration depth at different radiation intensity of steady state.