The authors deduced Gaussian function of millimeter wave power distribution, and built up a transient thermal multilayer model for the heating of murine skin by high power millimeter waves with finite volume method (FVM) based on HBHE in the present paper. We analyzed the calculated results and compared them with the results calculated by Pennes' equation and the experimental ones; found that the temperature calculated by HBHE was more reasonable. Especially under high power millimeter wave, the calculated results were basically consistent with the experimental ones, and the superiority of the theoretical model was confirmed.