＇Size segregation＇ is a typical phenomenon usually accompanied with flow of particles. It has been demonstrated experimentally and macroscopically. However, the microscopic mechanism is difficult to observe, and it is not understood sufficiently. In this study, the experiment focused on size segregation simulated using the distinct element method. A 2-dimensional simulation for the full model of the experiment indicates equivalent behavior. However, size segregation in an accumulated layer is not properly shown. Next, the simple partial model is simulated using 2- and 3-dimensional analysis. The 2-D result does not show the size segregation clearly due to the wide scattering of data, but that of 3-D shows that it is possible to simulate the segregation properly. Also, detailed observation of the movement of each particle demonstrates the validity of the mechanism of size segregation which was presented from the experiment.