Radiofrequency ablation is increasingly being used for liver cancer because it is a minimally invasive treatment method. However, it is difficult for the operators to precisely control the formation of coagulation zones because of the cooling effect of capillary vessels. To overcome this limitation, we have proposed a model-based robotic ablation system using a real-time numerical simulation to analyze temperature distributions in the target organ. This robot can determine the adequate amount of electric power supplied to the organ based on real-time temperature information reflecting the cooling effect provided by the simulator. The objective of this study was to develop a method to estimate the intraoperative rate of blood flow in the target organ to determine temperature distribution. In this paper, we propose a simulation-based method to estimate the rate of blood flow. We also performed an in vitro study to validate the proposed method by estimating the rate of blood flow in a hog liver. The experimental results revealed that the proposed method can be used to estimate the rate of blood flow in an organ.