In most previous models, simulation of the temperature generation in tissue is based on the Pennes bio-heat transfer equation, which implies an instantaneous thermal energy deposition in the medium. Due to the long thermal relaxation time τ (20 s–30 s) in biological tissues, the actual temperature elevation during clinical treatments could be different from the value predicted by the Pennes bioheat equation. The thermal wave model of bio-heat transfer (TWMBT) defines a thermal relaxation time to describe the tissue heating from ultrasound exposure. In this paper, COMSOL Multiphysics 3.5a, a finite element method software package, is used to simulate the temperature response in tissues based on Pennes and TWMBT equations. We further discuss different factors in the bio-heat transfer model on the influence of the temperature rising and it is found that the temperature response in tissue under ultrasound exposure is a rising process with a declining rate. The thermal relaxation time inhibits the temperature elevation at the beginning of ultrasonic heating. Besides, thermal relaxation in TWMBT leads to lower temperature estimation than that based on Pennes equation during the same period of time. The blood flow carrying heat dominates most to the decline of temperature rising rate and the influence increases with temperature rising. On the contrary, heat diffusion, which can be described by thermal conductivity, has little effect on the temperature rising.