A finite element method (FEM)-based thermal approach to reconstruct the disease-associated heat source distribution has been developed. The congruent relationship between the heat sources and the observed temperature is established from the FEM solution matrix. The regularization method based parameter iteration algorithm is further developed to solve the inverse bioheat transfer problems. Typical simulations on sphere model and real digital human head have been performed to validate the feasibility and efficacy of the current method. In addition, the regularization parameter is optimized to speed up the reconstruction process and reduce the thermal noises. All the results indicate that both the heat source distribution and three-dimensional (3D) temperature field within the biological body were successfully reconstructed with acceptable accuracy.