The vibrating motion of a particle bed and percolation of a tracer particle with relatively small size in the cyclic vibrating field are investigated using two-and three-dimensional simulation techniques based an the particle element method (PEM). The vibration and percolation behavior are influenced by the dimension in the simulation. That is, the particles motion simulated three dimensionally is animated in comparison with that simulated two dimensionally. In addition, the three dimensional simulation enables us to cause a mutual exchange of particles in the bed. On the other hand, the tracer particle is percolated towards the bottom of the bed in the three dimensional simulation, while it remains in the vicinity of the surface layer in the two dimensional one. According to the model analysis of the rearranging distance of particles in the bed in which the tracer is able to percolate into the bed, the distance analyzed three dimensionally is wider than that analyzed two dimensionally The discrepancy in the vibration and percolation behavior is attributed to the difference in the two and three dimensional porosity and their space structure formed in the vibrating bed.