In recent year, robotics and computer technology introduced in surgical domain allow surgery to be performed more precise medical care. In particular, computer technology enables precise surgical simulation using virtual reality or computer graphics. In our research, we will focus on constructing an intra-operative navigation system with online information of organs and surgical tools based on surgical simulation with mechanical models. This proposed simulation system consists of two simulators and an actual manipulator: virtual slave manipulator, organs deformation calculator and master controller. In this paper, we illustrated the organs deformation calculator and an experiment with pig liver and this simulator.