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With the benefits of high accuracy and non-invasive implementation, high intensity focused ultrasound (HIFU) is a promising medical procedure to heat and destroy pathogenic tissue rapidly. However, the relation between the power emitted by the ultrasound transducer and the energy arriving at the target area is complex, interfered by several factors such as the properties of tissue, obstacles of hard tissues or vascularization. In this study, a finite element model was used to simulate the propagation process of focused ultrasound inside tissue phantom and passing the perfused vascular. Then, the resultant sound pressure distribution provided the heat source for heat transfer process simulation. The simulation results were validated with thermocouple measurements in egg white phantoms. This study demonstrated an efficient methodology for estimating the thermal effects in HIFU hyperthermia therapy, especially in the region with large blood vessel. This study will be useful in minimizing difficulties and risks in HIFU induced hyperthermia treatment and facilitate the extension from laboratory to clinic use.