Realistic behavior in Computer Simulation of biological system (e.g. humans organs) is essential to 3D modeling in medicine. In order to improve realistic responses of 3D organ model it is essential to use mechanical models that can deal with multiple objects internal and external interactions in a reasonable time frame. We will apply the Smooth Particles Hydrodynamics (SPH) to model the esophagus and the stomach, thus constructing a physical background for interaction. We used a multilayer model of particles related to a single triangle mesh. Each particle layers represent distinct biological tissues of the esophagus and the stomach.