Medical technology has advanced with the introduction of robot technology, making previous medical treatments that were very difficult far more possible. However, operation of a surgical robot demands substantial training and continual practice on the part of the surgeon because it requires difficult techniques that are different from those of traditional surgical procedures. So we focused on a simulation technology based on the physical characteristics of organs as an intra-operative assistance for a surgeon. In this research, we proposed the development of surgical simulation, using a physical model, for intra-operative navigation. In this paper, we describe the design of our proposed system, in particular our organ deformation calculator. We performed two experiments with pig liver and silicone model to evaluate the accuracy of the calculator. We obtained adequate experimental results of a target node at a nearby point of interaction, because this point ensures better accuracy for our simulation model.