In the process of thermal ablation of tumors, the accurate control of the temperature for tumor and normal tissue plays a key role in the surgery. In order to accurately predict the temperature and heat flux for long-term observation, this paper presents a numerical model based on the smoothed finite element methods (SFEMs) for solving Pennes equation that describes the bioheat transfer problems. The smoothed Galerkin weak forms for Pennes equation are established, and the S-FEM models based on different time integration schemes are then formulated for unsteady bioheat transfer problems. The proposed model has been used to obtain the temperature distribution of the tissues with tumors during the surgery of thermal ablation, and the equivalent thermal energy and heat flux are also discussed. Through the results of the numerical analysis, the proposed smoothed finite element model can fast solve the bioheat transfer problem undergoing long-term changes and can improve the accuracy of temperature and efficiency of computation. It reconstructs the temperature gradient with high accuracy and performs better on the equivalent thermal energy. Besides, the model is more suitable for biological tissues with complex problem domains because it is less sensitive to the distortion of elements.