This paper presents a new method for simulating the deformation of organ models by using a neural network. The proposed method is based on the idea proposed by Chen et al. that a deformed model can be estimated from the superposition of basic deformation modes. The neural network finds a relationship between external forces and the models deformed by the forces. The experimental results show that the trained network can achieve a real-time simulation while keeping the acceptable accuracy compared with the nonlinear FEM computation.